title: RAW Control Rep3

description:
SAMPLE 3
RAW264.7 macrophage No treatment


title: HV-015 -0

status: Public on Jan 05 2017

type: RNA

city: Philadelphia

first: Annamarie

middle: D

last: Horan

state: PA

address: 3737 Market Street, 6th Floor

department: Orthopaedic Surgery

country: USA

institute: University of Pennsylvania

description: Healthy volunteer #15

hyb_protocol: Labeled  RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 1.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 640. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: GeneChip 3000 7G scanner with software version AGCC.

data_processing: Partek Genomics Suite, version 6.6 or lower was used to import data using Quartile Normalization, Median Polish summarization. ANOVA with multiple test correction (with a stepped up p value of 0.05 to 0.1 and fold change ± 1.5) was used for discovery rather than statistical purposes, with repeated measures of Acutely Injured Subjects (AIS) included in the analysis to identify potential miRNAs that were differentially expressed between AIS and healthy volunteers.  We then validated performance on RT-qPCR.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole venous blood

label_protocol: Affymetrix FlashTag™ Biotin RNA Labeling Kit

growth_protocol: Not applicable

extract_protocol: PaxGene microRNA Isolation kit

treatment_protocol: Not applicable for healthy volunteers.  Standard care surgery for Acutely Injured.

tag: Sex

value: Female

tag: age

tag: race

value: Black

tag: stress

value: healthy


title: HV-020 -0

description: Healthy volunteer #20


title: HV-013 -0

description: Healthy volunteer #13

value: White


title: HV-014 -0

description: Healthy volunteer #14


title: HV-017 -0

description: Healthy volunteer #17

value: Male


title: HV-019 -0

description: Healthy volunteer #19


title: HV-008 -0

description: Healthy volunteer #8


title: HV-011 -0

description: Healthy volunteer #11


title: HV-003 -0

description: Healthy volunteer #3


title: HV-001 -0

description: Healthy volunteer #1


title: HV-012 -0

description: Healthy volunteer #12

value: Asian


title: HV-005 -0

description: Healthy volunteer #5


title: HV-006 -0

description: Healthy volunteer #6


title: AIS-007-7

description: Acutely injured subject #7 Day 7

value: acutely injured

tag: day


title: AIS-006-5

description: Acutely injured subject #6 Day 5


title: AIS-005-4

description: Acutely injured subject #5Day 4


title: AIS-006-6

description: Acutely injured subject #6 Day 6


title: AIS-002-90

description: Acutely injured subject #2 Day 90


title: AIS-003-6

description: Acutely injured subject #3 Day 6


title: AIS-005-3

description: Acutely injured subject #5 Day 3


title: AIS-004-7

description: Acutely injured subject #4 Day 7


title: AIS-001-90

description: Acutely injured subject #1 Day 90


title: 22329.DR.2 (82.2)

city: Columbia

first: Elizabeth

middle: G

last: King

state: MO

address: 105 Tucker Hall

department: Biological Sciences

institute: University of Missouri

data_processing: We used Ribosomal Protein L32 (RPL32) to normalize our expression measures using 2^-ΔCq. All fold changes were calculated relative to the control diet using 2^-ΔΔCq.

organism: Drosophila melanogaster

source_name: whole fly

label_protocol: Applied Biosystems High Capacity Reverse Transcription kit

growth_protocol: Temperature: 23C; Humidity: 50%; Light cycle 24:0

extract_protocol: Trizol extraction followed by a Qiagen clean up

tag: recombinant inbred line

tag: treatment

value: dietary restrictions

tag: batch

value: batch 2


title: HV-007 -0

description: Healthy volunteer #7


title: 22177.C.2 (90.2)

value: control


title: 22395.C.2 (795.2)


title: 22024.C.2 (792.2)


title: 22069.DR.2 (793.2)


title: 22022.HS.2 (794.2)

value: high sugar


title: 22022.DR.2 (791.2)


title: 22035.C.2 (790.2)


title: 22036.C.2 (788.2)


title: 22080.HS.2 (784.2)


title: 22004.C.2 (786.2)


title: 22038.C.2 (787.2)


title: 22035.DR.2 (783.2)


title: 22033.C.2 (782.2)


title: Treated_Bio_Replicate 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression on treatment with PGPR after 48 hrs

hyb_protocol: 1650ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to Agilent designed Rice Gene expression Microarray 4x44K (AMADID No: G2514F_064815) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 3 micron resolution.

data_processing: Images were quantified using Feature Extraction Software ( Agilent).

organism: Oryza sativa

source_name: Root tissue treated with PGPR

label_protocol: The samples for gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasyMini kit columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000

growth_protocol: Seedlings germinated in MS media

extract_protocol: RNA isolation was done by using QIAGEN RNeasy mini kit (Cat#74904)  as per the manufacturer’s protocols.

treatment_protocol: Plantlets transferred to Hoagland's solution and treated with B.subtilis

tag: tissue

value: root

tag: treatment period

value: 48 hours


title: 22036.HS.2 (781.2)


title: 22069.HS.2 (780.2)


title: Control_Bio_Replicate 3

description: Gene expression after 48 hrs

source_name: Control Root tissue


title: Treated_Bio_Replicate 3


title: 22004.HS.2 (779.2)


title: Control_Bio_Replicate 1

description: Gene expression after 48 hrs


title: 22024.DR.2 (778.2)


title: Control_Bio_Replicate 2

description: Gene expression after 48 hrs


title: Treated_Bio_Replicate 1


title: 22433.C.2 (769.2)


title: 22004.DR.2 (789.2)


title: 22046.HS.2 (773.2)


title: 22219.HS.2 (765.2)


title: 22033.HS.2 (775.2)


title: 22039.C.2 (785.2)


title: 22046.DR.2 (777.2)


title: 22429.HS.2 (771.2)


title: 22433.DR.2 (770.2)


title: 22024.HS.2 (774.2)


title: 22324.C.2 (768.2)


title: 22092.C.2 (767.2)


title: 22219.HS.2 (772.2)


title: 22100.HS.2 (766.2)


title: 22038.HS.2 (776.2)


title: 22354.DR.2 (764.2)


title: 22075.C.2 (761.2)


title: 22195.C.2 (760.2)


title: 22227.DR.2 (762.2)


title: 22338.HS.2 (759.2)


title: 22223.HS.2 (758.2)


title: 22206.C.2 (755.2)


title: 22165.DR.2 (753.2)


title: 22222.HS.2 (756.2)


title: 22222.C.2 (751.2)


title: 22332.C.2 (763.2)


title: 22332.HS.2 (750.2)


title: 22240.C.2 (746.2)


title: 22129.DR.2 (744.2)


title: 22212.DR.2 (748.2)


title: 22206.DR.2 (743.2)


title: 22335.C.2 (715.2)


title: 22075.HS.2 (691.2)


title: 22348.DR.2 (747.2)


title: 22100.C.2 (697.2)


title: 22390.C.2 (670.2)


title: 22395.C.2 (676.2)


title: 22374.C.2 (757.2)


title: 22092.DR.2 (666.2)


title: 22165.HS.2 (665.2)


title: 22335.HS.2 (684.2)


title: 22119.HS.2 (663.2)


title: 22338.C.2 (752.2)


title: 22096.C.2 (658.2)


title: 22091.HS.2 (661.2)


title: 22092.HS.2 (754.2)


title: 22146.HS.2 (653.2)


title: 22154.DR.2 (647.2)


title: 22119.C.2 (617.2)


title: 22219.C.2 (749.2)


title: 22210.C.2 (745.2)


title: 22251.C.2 (6.2)


title: 22168.HS.2 (599.2)


title: 22054.C.2 (681.2)


title: 22101.HS.2 (595.2)


title: 22083.DR.2 (597.2)


title: 22109.DR.2 (587.2)


title: 22189.HS.2 (536.2)


title: 22144.C.2 (571.2)


title: 22361.DR.2 (65.2)


title: 22108.HS.2 (529.2)


title: 22158.DR.2 (578.2)


title: 22118.DR.2 (498.2)


title: 22185.HS.2 (500.2)


title: 22209.HS.2 (483.2)


title: 22170.DR.2 (524.2)


title: 22248.DR.2 (520.2)


title: 22028.HS.2 (515.2)


title: 22246.HS.2 (519.2)


title: 22237.HS.2 (475.2)


title: 22089.DR.2 (469.2)


title: 22156.C.2 (463.2)


title: 22259.DR.2 (46.2)


title: 22203.DR.2 (45.2)


title: 22243.C.2 (47.2)


title: 22307.DR.2 (42.2)


title: 22235.C.2 (439.2)


title: 22052.DR.2 (420.2)


title: 22077.C.2 (419.2)


title: 22057.HS.2 (417.2)


title: 22084.DR.2 (413.2)


title: 22039.DR.2 (416.2)


title: 22014.C.2 (414.2)


title: 22235.HS.2 (478.2)


title: 22118.HS.2 (476.2)


title: 22060.C.2 (407.2)


title: 22014.DR.2 (405.2)


title: 22039.HS.2 (410.2)


title: 22057.C.2 (404.2)


title: 22418.DR.2 (399.2)


title: 22052.HS.2 (406.2)


title: 22060.HS.2 (402.2)


title: 22157.HS.2 (395.2)


title: 22452.HS.2 (394.2)


title: 22345.DR.2 (391.2)


title: 22077.DR.2 (418.2)


title: 22084.HS.2 (408.2)


title: 22014.HS.2 (409.2)


title: 22065.C.2 (390.2)


title: 22035.HS.2 (403.2)


title: 22057.DR.2 (401.2)


title: 22137.HS.2 (385.2)


title: 22260.DR.2 (384.2)


title: 22239.HS.2 (388.2)


title: 22369.C.2 (383.2)


title: 22062.C.2 (375.2)


title: 22224.DR.2 (382.2)


title: 22137.DR.2 (380.2)


title: 22454.HS.2 (373.2)


title: 22380.DR.2 (351.2)


title: 22441.HS.2 (369.2)


title: 22430.HS.2 (356.2)


title: 22430.DR.2 (398.2)


title: 22464.C.2 (396.2)


title: 22239.DR.2 (344.2)


title: 22439.C.2 (389.2)


title: 22408.C.2 (343.2)


title: 22439.DR.2 (335.2)


title: 22369.HS.2 (331.2)


title: 22462.DR.2 (318.2)


title: 22017.DR.2 (290.2)


title: 22299.DR.2 (29.2)


title: 22457.HS.2 (294.2)


title: 22183.HS.2 (289.2)


title: 22396.DR.2 (280.2)


title: 22384.DR.2 (284.2)


title: 22392.C.2 (288.2)


title: 22142.C.2 (27.2)


title: 22385.C.2 (277.2)


title: 22295.C.2 (258.2)


title: 22293.C.2 (254.2)


title: 22281.DR.2 (252.2)


title: 22469.C.2 (250.2)


title: 22293.HS.2 (236.2)


title: 22111.DR.2 (239.2)


title: 22458.C.2 (225.2)


title: 22295.HS.2 (219.2)


title: 22440.C.2 (217.2)


title: 22266.DR.2 (220.2)


title: 22460.HS.2 (242.2)


title: 22423.DR.2 (342.2)


title: 22461.HS.2 (307.2)


title: 22469.DR.2 (211.2)


title: 22442.DR.2 (209.2)


title: 22269.HS.2 (208.2)


title: 22466.HS.2 (329.2)


title: 22294.C.2 (205.2)


title: 22295.DR.2 (201.2)


title: 22460.C.2 (200.2)


title: 22463.DR.2 (202.2)


title: 22469.HS.2 (180.2)


title: 22293.DR.2 (183.2)


title: 22406.C.2 (189.2)


title: 22381.HS.2 (166.2)


title: 22131.HS.2 (157.2)


title: 22203.C.2 (159.2)


title: 22316.C.2 (153.2)


title: 22319.HS.2 (158.2)


title: 22249.DR.2 (133.2)


title: 22307.C.2 (148.2)


title: 22329.C.2 (135.2)


title: 22307.HS.2 (106.2)


title: 22339.C.2 (107.2)


title: 22238.HS.1 (99.1)

value: batch 1


title: 22326.C.2 (11.2)


title: 22259.HS.2 (12.2)


title: 22243.DR.1 (97.1)


title: 22206.HS.1 (92.1)


title: 22184.DR.1 (96.1)


title: 22315.HS.1 (93.1)


title: 22223.DR.1 (95.1)


title: 22249.HS.1 (98.1)


title: 22184.C.1 (9.1)


title: 22230.C.1 (94.1)


title: 22326.DR.1 (91.1)


title: 22177.C.1 (90.1)


title: 22251.HS.1 (88.1)


title: 22298.C.1 (89.1)


title: 22223.C.1 (87.1)


title: 22305.HS.1 (85.1)


title: 22339.HS.1 (84.1)


title: 22370.DR.1 (83.1)


title: 22300.HS.2 (126.2)


title: 22316.HS.1 (81.1)


title: 22329.DR.1 (82.1)


title: 22306.HS.1 (8.1)


title: 22350.C.1 (80.1)


title: 22131.C.1 (79.1)


title: 22315.C.1 (86.1)


title: 22208.HS.1 (741.1)


title: 22243.HS.1 (77.1)


title: 22379.DR.1 (738.1)


title: 22075.DR.1 (731.1)


title: 22195.DR.1 (736.1)


title: 22223.DR.1 (735.1)


title: 22100.DR.1 (740.1)


title: 22324.DR.1 (728.1)


title: 22343.C.1 (75.1)


title: 22213.DR.1 (727.1)


title: 22395.HS.1 (733.1)


title: 22329.C.1 (734.1)


title: 22212.C.1 (73.1)


title: 22212.HS.1 (732.1)


title: 22149.HS.1 (76.1)


title: 22205.HS.1 (74.1)


title: 22390.DR.1 (739.1)


title: 22165.C.1 (742.1)


title: 22054.DR.1 (725.1)


title: 22347.DR.1 (729.1)


title: 22374.DR.1 (730.1)


title: 22379.HS.1 (737.1)


title: 22332.DR.1 (722.1)


title: 22348.HS.1 (723.1)


title: 22227.HS.1 (721.1)


title: 22181.DR.1 (72.1)


title: 22240.HS.1 (720.1)


title: 22195.HS.1 (724.1)


title: 22347.C.1 (719.1)


title: 22367.C.1 (726.1)


title: 22176.C.1 (717.1)


title: 22210.DR.1 (714.1)


title: 22358.C.1 (718.1)


title: 22210.HS.1 (712.1)


title: 22379.C.1 (711.1)


title: 22054.HS.1 (704.1)


title: 22370.C.1 (71.1)


title: 22213.HS.1 (716.1)


title: 22212.C.1 (710.1)


title: 22322.HS.1 (708.1)


title: 22176.HS.1 (706.1)


title: 22335.C.1 (715.1)


title: 22358.HS.1 (705.1)


title: 22348.C.1 (713.1)


title: 22213.C.1 (707.1)


title: 22351.DR.1 (709.1)


title: 22324.HS.1 (695.1)


title: 22208.DR.1 (696.1)


title: 22208.C.1 (702.1)


title: 22395.DR.1 (700.1)


title: 22061.DR.1 (701.1)


title: 22100.C.1 (697.1)


title: 22329.DR.1 (699.1)


title: 22339.DR.1 (7.1)


title: 22367.HS.1 (698.1)


title: 22347.HS.1 (703.1)


title: 22249.C.1 (70.1)


title: 22061.HS.1 (694.1)


title: 22390.HS.1 (693.1)


title: 22354.HS.1 (692.1)


title: 22075.HS.1 (691.1)


title: 22219.C.1 (69.1)


title: 22322.C.1 (686.1)


title: 22240.DR.1 (688.1)


title: 22227.C.1 (690.1)


title: 22351.HS.1 (682.1)


title: 22335.DR.1 (678.1)


title: 22354.C.1 (685.1)


title: 22322.DR.1 (687.1)


title: 22338.DR.1 (689.1)


title: 22054.C.1 (681.1)


title: 22335.HS.1 (684.1)


title: 22176.DR.1 (677.1)


title: 22222.DR.1 (669.1)


title: 22219.DR.1 (680.1)


title: 22351.C.1 (674.1)


title: 22223.C.1 (683.1)


title: 22395.C.1 (676.1)


title: 22061.C.1 (671.1)


title: 22367.DR.1 (679.1)


title: 22129.C.1 (667.1)


title: 22219.DR.1 (68.1)


title: 22374.HS.1 (672.1)


title: 22129.HS.1 (668.1)


title: 22358.DR.1 (673.1)


title: 22329.HS.1 (675.1)


title: 22390.C.1 (670.1)


title: 22165.HS.1 (665.1)


title: 22092.DR.1 (666.1)


title: 22262.HS.1 (67.1)


title: 22166.C.1 (660.1)


title: 22091.HS.1 (661.1)


title: 22102.C.1 (662.1)


title: 22096.C.1 (658.1)


title: 22102.DR.1 (657.1)


title: 22206.HS.1 (664.1)


title: 22096.DR.1 (656.1)


title: 22119.HS.1 (663.1)


title: 22144.DR.1 (659.1)


title: 22257.DR.1 (66.1)


title: 22146.HS.1 (653.1)


title: 22154.DR.1 (647.1)


title: 22109.HS.1 (652.1)


title: 22361.DR.1 (65.1)


title: 22136.DR.1 (646.1)


title: 22119.DR.1 (648.1)


title: 22072.HS.1 (654.1)


title: 22072.DR.1 (649.1)


title: 22125.C.1 (640.1)


title: 22179.HS.1 (642.1)


title: 22163.HS.1 (644.1)


title: 22121.C.1 (645.1)


title: 22181.C.1 (64.1)


title: 22148.C.1 (655.1)


title: 22152.DR.1 (651.1)


title: 22134.DR.1 (639.1)


title: 22152.HS.1 (643.1)


title: 22163.DR.1 (650.1)


title: 22136.HS.1 (638.1)


title: 22150.DR.1 (635.1)


title: 22148.DR.1 (641.1)


title: 22172.DR.1 (636.1)


title: 22187.C.1 (634.1)


title: 22191.HS.1 (632.1)


title: 22146.C.1 (631.1)


title: 22167.DR.1 (629.1)


title: 22158.HS.1 (637.1)


title: 22088.HS.1 (630.1)


title: 22121.HS.1 (628.1)


title: 22101.DR.1 (633.1)


title: 22123.DR.1 (621.1)


title: 22083.HS.1 (624.1)


title: 22191.DR.1 (622.1)


title: 22150.C.1 (625.1)


title: 22168.C.1 (620.1)


title: 22113.DR.1 (619.1)


title: 22119.C.1 (617.1)


title: 22178.C.1 (618.1)


title: 22123.C.1 (614.1)


title: 22088.DR.1 (616.1)


title: 22098.DR.1 (613.1)


title: 22134.C.1 (612.1)


title: 22121.DR.1 (627.1)


title: 22135.DR.1 (623.1)


title: 22099.DR.1 (611.1)


title: 22150.HS.1 (626.1)


title: 22143.C.1 (610.1)


title: 22350.DR.1 (61.1)


title: 22349.HS.1 (62.1)


title: 22083.C.1 (607.1)


title: 22154.C.1 (608.1)


title: 22091.DR.1 (606.1)


title: 22163.C.1 (605.1)


title: 22098.C.1 (603.1)


title: 22154.HS.1 (604.1)


title: 22366.C.1 (63.1)


title: 22251.C.1 (6.1)


title: 22238.C.1 (60.1)


title: 22159.C.1 (615.1)


title: 22099.C.1 (598.1)


title: 22168.HS.1 (599.1)


title: 22101.HS.1 (595.1)


title: 22187.DR.1 (609.1)


title: 22178.DR.1 (596.1)


title: 22178.HS.1 (594.1)


title: 22191.C.1 (592.1)


title: 22143.HS.1 (602.1)


title: 22167.HS.1 (591.1)


title: 22113.HS.1 (593.1)


title: 22159.HS.1 (590.1)


title: 22311.DR.1 (59.1)


title: 22134.HS.1 (589.1)


title: 22109.DR.1 (587.1)


title: 22115.HS.1 (601.1)


title: 22172.C.1 (586.1)


title: 22152.C.1 (600.1)


title: 22179.C.1 (585.1)


title: 22159.DR.1 (588.1)


title: 22166.DR.1 (584.1)


title: 22139.C.1 (581.1)


title: 22083.DR.1 (597.1)


title: 22088.C.1 (579.1)


title: 22376.C.1 (58.1)


title: 22158.C.1 (580.1)


title: 22096.HS.1 (576.1)


title: 22102.HS.1 (577.1)


title: 22123.HS.1 (574.1)


title: 22158.DR.1 (578.1)


title: 22187.HS.1 (573.1)


title: 22144.C.1 (571.1)


title: 22143.DR.1 (572.1)


title: 22146.DR.1 (570.1)


title: 22115.DR.1 (569.1)


title: 22257.HS.1 (57.1)


title: 22125.HS.1 (567.1)


title: 22113.C.1 (582.1)


title: 22139.HS.1 (568.1)


title: 22099.HS.1 (583.1)


title: 22167.C.1 (561.1)


title: 22091.C.1 (564.1)


title: 22101.C.1 (565.1)


title: 22135.HS.1 (566.1)


title: 22115.C.1 (560.1)


title: 22148.HS.1 (559.1)


title: 22306.DR.1 (56.1)


title: 22136.C.1 (556.1)


title: 22166.HS.1 (557.1)


title: 22179.DR.1 (558.1)


title: 22139.DR.1 (562.1)


title: 22098.HS.1 (555.1)


title: 22125.DR.1 (575.1)


title: 22135.C.1 (552.1)


title: 22144.HS.1 (554.1)


title: 22109.C.1 (551.1)


title: 22168.DR.1 (550.1)


title: 22140.DR.1 (548.1)


title: 22066.C.1 (547.1)


title: 22241.HS.1 (549.1)


title: 22066.DR.1 (546.1)


title: 22172.HS.1 (563.1)


title: 22118.C.1 (543.1)


title: 22112.HS.1 (542.1)


title: 22140.HS.1 (540.1)


title: 22018.DR.1 (544.1)


title: 22221.DR.1 (541.1)


title: 22241.C.1 (545.1)


title: 22072.C.1 (553.1)


title: 22138.HS.1 (54.1)


title: 22190.HS.1 (535.1)


title: 22090.C.1 (539.1)


title: 22202.DR.1 (538.1)


title: 22221.C.1 (537.1)


title: 22189.HS.1 (536.1)


title: 22202.HS.1 (534.1)


title: 22009.DR.1 (531.1)


title: 22209.DR.1 (533.1)


title: 22366.HS.1 (53.1)


title: 22108.HS.1 (529.1)


title: 22025.DR.1 (530.1)


title: 22025.HS.1 (532.1)


title: 22037.HS.1 (528.1)


title: 22361.HS.1 (55.1)


title: 22185.C.1 (526.1)


title: 22170.DR.1 (524.1)


title: 22120.C.1 (523.1)


title: 22232.HS.1 (522.1)


title: 22049.HS.1 (521.1)


title: 22298.HS.1 (52.1)


title: 22124.HS.1 (517.1)


title: 22221.HS.1 (518.1)


title: 22090.HS.1 (516.1)


title: 22028.HS.1 (515.1)


title: 22193.HS.1 (514.1)


title: 22145.HS.1 (511.1)


title: 22124.C.1 (508.1)


title: 22185.DR.1 (510.1)


title: 22120.DR.1 (513.1)


title: 22120.HS.1 (527.1)


title: 22237.C.1 (525.1)


title: 22182.C.1 (512.1)


title: 22182.HS.1 (509.1)


title: 22028.DR.1 (506.1)


title: 22376.HS.1 (51.1)


title: 22217.DR.1 (505.1)


title: 22042.C.1 (507.1)


title: 22226.C.1 (503.1)


title: 22182.DR.1 (502.1)


title: 22193.DR.1 (504.1)


title: 22185.HS.1 (500.1)


title: 22342.HS.1 (50.1)


title: 22212.HS.1 (5.1)


title: 22246.HS.1 (519.1)


title: 22145.DR.1 (499.1)


title: 22118.DR.1 (498.1)


title: 22018.C.1 (496.1)


title: 22124.DR.1 (495.1)


title: 22237.DR.1 (494.1)


title: 22190.C.1 (493.1)


title: 22376.DR.1 (49.1)


title: 22029.HS.1 (491.1)


title: 22066.HS.1 (488.1)


title: 22193.C.1 (501.1)


title: 22217.HS.1 (487.1)


title: 22042.HS.1 (484.1)


title: 22114.HS.1 (490.1)


title: 22228.HS.1 (482.1)


title: 22226.DR.1 (477.1)


title: 22118.HS.1 (476.1)


title: 22235.HS.1 (478.1)


title: 22228.DR.1 (479.1)


title: 22263.C.1 (48.1)


title: 22106.HS.1 (481.1)


title: 22009.HS.1 (485.1)


title: 22209.HS.1 (483.1)


title: 22237.HS.1 (475.1)


title: 22156.HS.1 (480.1)


title: 22049.DR.1 (489.1)


title: 22114.DR.1 (486.1)


title: 22170.HS.1 (471.1)


title: 22030.C.1 (473.1)


title: 22189.C.1 (492.1)


title: 22243.C.1 (47.1)


title: 22104.C.1 (497.1)


title: 22114.C.1 (468.1)


title: 22089.DR.1 (469.1)


title: 22235.DR.1 (472.1)


title: 22028.C.1 (466.1)


title: 22156.C.1 (463.1)


title: 22108.DR.1 (461.1)


title: 22029.DR.1 (464.1)


title: 22042.DR.1 (465.1)


title: 22217.C.1 (474.1)


title: 22259.DR.1 (46.1)


title: 22009.C.1 (454.1)


title: 22214.DR.1 (462.1)


title: 22209.C.1 (456.1)


title: 22090.DR.1 (457.1)


title: 22095.DR.1 (455.1)


title: 22029.C.1 (451.1)


title: 22246.C.1 (470.1)


title: 22214.C.1 (452.1)


title: 22106.DR.1 (450.1)


title: 22170.C.1 (453.1)


title: 22106.C.1 (459.1)


title: 22203.DR.1 (45.1)


title: 22248.C.1 (449.1)


title: 22228.C.1 (448.1)


title: 22037.DR.1 (446.1)


title: 22202.C.1 (447.1)


title: 22104.DR.1 (443.1)


title: 22025.C.1 (445.1)


title: 22030.DR.1 (444.1)


title: 22214.HS.1 (441.1)


title: 22049.C.1 (440.1)


title: 22112.DR.1 (437.1)


title: 22246.DR.1 (436.1)


title: 22030.HS.1 (467.1)


title: 22095.C.1 (435.1)


title: 22156.DR.1 (432.1)


title: 22190.DR.1 (433.1)


title: 22095.HS.1 (431.1)


title: 22235.C.1 (439.1)


title: 22189.DR.1 (460.1)


title: 22167.DR.1 (44.1)


title: 22018.HS.1 (434.1)


title: 22089.HS.1 (438.1)


title: 22232.C.1 (427.1)


title: 22241.DR.1 (430.1)


title: 22140.C.1 (429.1)


title: 22089.C.1 (428.1)


title: 22112.C.1 (426.1)


title: 22342.C.1 (43.1)


title: 22226.HS.1 (425.1)


title: 22145.C.1 (424.1)


title: 22104.HS.1 (442.1)


title: 22232.DR.1 (422.1)


title: 22307.DR.1 (42.1)


title: 22052.DR.1 (420.1)


title: 22248.HS.1 (421.1)


title: 22077.C.1 (419.1)


title: 22037.C.1 (423.1)


title: 22057.HS.1 (417.1)


title: 22052.C.1 (415.1)


title: 22039.DR.1 (416.1)


title: 22084.DR.1 (413.1)


title: 22014.C.1 (414.1)


title: 22077.DR.1 (418.1)


title: 22077.HS.1 (411.1)


title: 22014.HS.1 (409.1)


title: 22379.C.1 (41.1)


title: 22060.DR.1 (412.1)


title: 22060.C.1 (407.1)


title: 22052.HS.1 (406.1)


title: 22039.HS.1 (410.1)


title: 22084.HS.1 (408.1)


title: 22014.DR.1 (405.1)


title: 22057.DR.1 (401.1)


title: 22213.HS.1 (4.1)


title: 22057.C.1 (404.1)


title: 22084.C.1 (400.1)


title: 22325.DR.1 (40.1)


title: 22430.DR.1 (398.1)


title: 22418.DR.1 (399.1)


title: 22060.HS.1 (402.1)


title: 22464.C.1 (396.1)


title: 22457.DR.1 (397.1)


title: 22157.HS.1 (395.1)


title: 22452.HS.1 (394.1)


title: 22218.DR.1 (393.1)


title: 22445.C.1 (392.1)


title: 22108.C.1 (458.1)


title: 22345.DR.1 (391.1)


title: 22065.C.1 (390.1)


title: 22326.HS.1 (39.1)


title: 22239.HS.1 (388.1)


title: 22062.HS.1 (386.1)


title: 22439.C.1 (389.1)


title: 22439.HS.1 (387.1)


title: 22132.HS.1 (377.2)


title: 22369.C.1 (383.1)


title: 22132.HS.1 (377.1)


title: 22137.HS.1 (385.1)


title: 22444.DR.1 (378.1)


title: 22137.DR.1 (380.1)


title: 22430.C.1 (379.1)


title: 22319.DR.1 (38.1)


title: 22355.C.1 (376.1)


title: 22355.C.1 (376.2)


title: 22260.DR.1 (384.1)


title: 22445.DR.1 (374.1)


title: 22224.HS.1 (371.1)


title: 22461.DR.1 (370.1)


title: 22425.C.1 (368.1)


title: 22441.HS.1 (369.1)


title: 22224.DR.1 (382.1)


title: 22418.HS.1 (372.1)


title: 22378.HS.1 (37.1)


title: 22345.HS.1 (367.1)


title: 22132.C.1 (381.1)


title: 22260.HS.1 (362.1)


title: 22017.C.1 (363.1)


title: 22426.HS.1 (364.1)


title: 22218.C.1 (361.1)


title: 22430.HS.1 (356.1)


title: 22062.C.1 (375.1)


title: 22355.HS.1 (360.1)


title: 22132.DR.1 (358.1)


title: 22183.C.1 (354.1)


title: 22362.HS.1 (353.1)


title: 22461.C.1 (352.1)


title: 22261.DR.1 (350.1)


title: 22065.HS.1 (359.1)


title: 22300.DR.1 (35.1)


title: 22467.C.1 (348.1)


title: 22380.DR.1 (351.1)


title: 22432.DR.1 (347.1)


title: 22408.C.1 (343.1)


title: 22441.C.1 (346.1)


title: 22423.DR.1 (342.1)


title: 22362.DR.1 (349.1)


title: 22380.HS.1 (355.1)


title: 22441.DR.1 (341.1)


title: 22423.C.1 (340.1)


title: 22457.C.1 (345.1)


title: 22319.C.1 (36.1)


title: 22212.DR.1 (34.1)


title: 22017.HS.1 (339.1)


title: 22439.DR.1 (335.1)


title: 22415.C.1 (332.1)


title: 22239.DR.1 (344.1)


title: 22466.HS.1 (329.1)


title: 22466.DR.1 (334.1)


title: 22464.DR.1 (327.1)


title: 22157.DR.1 (324.1)


title: 22157.C.1 (325.1)


title: 22065.DR.1 (323.1)


title: 22432.HS.1 (333.1)


title: 22380.C.1 (326.1)


title: 22426.DR.1 (322.1)


title: 22261.C.1 (321.1)


title: 22415.HS.1 (319.1)


title: 22369.DR.1 (320.1)


title: 22362.C.1 (317.1)


title: 22462.DR.1 (318.1)


title: 22452.C.1 (316.1)


title: 22444.C.1 (336.1)


title: 22224.C.1 (315.1)


title: 22218.HS.1 (338.1)


title: 22408.HS.1 (313.1)


title: 22369.HS.1 (331.1)


title: 22260.C.1 (330.1)


title: 22418.C.1 (328.1)


title: 22454.DR.1 (312.1)


title: 22408.DR.1 (311.1)


title: 22432.C.1 (309.1)


title: 22425.DR.1 (310.1)


title: 22461.HS.1 (307.1)


title: 22464.HS.1 (306.1)


title: 22454.C.1 (305.1)


title: 22213.C.1 (32.1)


title: 22062.DR.1 (304.1)


title: 22415.DR.1 (303.1)


title: 22425.HS.1 (314.1)


title: 22466.C.1 (298.1)


title: 22261.HS.1 (302.1)


title: 22423.HS.1 (299.1)


title: 22137.C.1 (296.1)


title: 22444.HS.1 (295.1)


title: 22457.HS.1 (294.1)


title: 22183.DR.1 (297.1)


title: 22462.C.1 (292.1)


title: 22379.DR.1 (31.1)


title: 22239.C.1 (291.1)


title: 22355.DR.1 (308.1)


title: 22467.HS.1 (293.1)


title: 22017.DR.1 (290.1)


title: 22345.C.1 (300.1)


title: 22138.C.1 (3.1)


title: 22383.C.1 (286.1)


title: 22395.DR.1 (287.1)


title: 22392.C.1 (288.1)


title: 22389.C.1 (283.1)


title: 22389.DR.1 (285.1)


title: 22299.DR.1 (29.1)


title: 22396.DR.1 (280.1)


title: 22300.C.1 (28.1)


title: 22401.DR.1 (281.1)


title: 22396.C.1 (282.1)


title: 22383.HS.1 (278.1)


title: 22397.DR.1 (279.1)


title: 22396.HS.1 (276.1)


title: 22395.HS.1 (274.1)


title: 22385.C.1 (277.1)


title: 22401.HS.1 (275.1)


title: 22183.HS.1 (289.1)


title: 22397.C.1 (272.1)


title: 22385.DR.1 (271.1)


title: 22392.HS.1 (270.1)


title: 22384.DR.1 (284.1)


title: 22384.C.1 (273.1)


title: 22142.C.1 (27.1)


title: 22391.C.1 (268.1)


title: 22391.DR.1 (269.1)


title: 22392.DR.1 (267.1)


title: 22391.HS.1 (266.1)


title: 22385.HS.1 (261.1)


title: 22389.HS.1 (262.1)


title: 22401.C.1 (265.1)


title: 22285.DR.1 (260.1)


title: 22251.DR.1 (26.1)


title: 22433.HS.1 (259.1)


title: 22383.DR.1 (263.1)


title: 22416.C.1 (257.1)


title: 22295.C.1 (258.1)


title: 22397.HS.1 (264.1)


title: 22420.DR.1 (255.1)


title: 22293.C.1 (254.1)


title: 22258.C.1 (25.1)


title: 22431.HS.1 (251.1)


title: 22281.DR.1 (252.1)


title: 22469.C.1 (250.1)


title: 22420.C.1 (249.1)


title: 22429.C.1 (253.1)


title: 22277.DR.1 (248.1)


title: 22446.C.1 (247.1)


title: 22288.C.1 (246.1)


title: 22453.HS.1 (243.1)


title: 22422.DR.1 (245.1)


title: 22452.DR.1 (301.1)


title: 22460.HS.1 (242.1)


title: 22463.C.1 (244.1)


title: 22281.C.1 (241.1)


title: 22094.HS.1 (256.1)


title: 22310.HS.1 (24.1)


title: 22111.DR.1 (239.1)


title: 22446.DR.1 (240.1)


title: 22463.HS.1 (237.1)


title: 22285.C.1 (235.1)


title: 22293.HS.1 (236.1)


title: 22442.C.1 (233.1)


title: 22277.HS.1 (232.1)


title: 22467.DR.1 (357.1)


title: 22288.DR.1 (231.1)


title: 22460.DR.1 (230.1)


title: 22304.HS.1 (23.1)


title: 22453.C.1 (229.1)


title: 22287.C.1 (226.1)


title: 22431.C.1 (227.1)


title: 22271.HS.1 (228.1)


title: 22458.C.1 (225.1)


title: 22468.HS.1 (224.1)


title: 22426.HS.1 (365.1)


title: 22417.HS.1 (223.1)


title: 22455.HS.1 (238.1)


title: 22446.HS.1 (222.1)


title: 22266.DR.1 (220.1)


title: 22445.HS.1 (366.1)


title: 22288.HS.1 (234.1)


title: 22177.DR.1 (22.1)


title: 22295.HS.1 (219.1)


title: 22440.C.1 (217.1)


title: 22294.DR.1 (221.1)


title: 22417.C.1 (216.1)


title: 22271.DR.1 (215.1)


title: 22266.C.1 (218.1)


title: 22419.DR.1 (212.1)


title: 22469.DR.1 (211.1)


title: 22287.DR.1 (210.1)


title: 22442.DR.1 (209.1)


title: 22277.C.1 (206.1)


title: 22149.C.1 (21.1)


title: 22468.C.1 (204.1)


title: 22460.C.1 (200.1)


title: 22429.DR.1 (214.1)


title: 22294.C.1 (205.1)


title: 22463.DR.1 (202.1)


title: 22419.C.1 (203.1)


title: 22295.DR.1 (201.1)


title: 22468.DR.1 (194.1)


title: 22310.DR.1 (20.1)


title: 22349.DR.1 (2.1)


title: 22269.DR.1 (192.1)


title: 22094.C.1 (198.1)


title: 22094.DR.1 (195.1)


title: 22420.HS.1 (196.1)


title: 22266.HS.1 (197.1)


title: 22453.DR.1 (213.1)


title: 22442.HS.1 (190.1)


title: 22142.DR.1 (19.1)


title: 22406.C.1 (189.1)


title: 22417.DR.1 (191.1)


title: 22416.HS.1 (188.1)


title: 22406.HS.1 (207.1)


title: 22271.C.1 (187.1)


title: 14286410 - Col-0::1390::MAS_BR1 vs Col-0_BR1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Transcriptomic changes induced by opine production in Arabidopsis thaliana grown in natural soil

hyb_protocol: Col-0_BR1 Cy5 / Col-0::1390::MAS_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: stem - Media=compost/Merantaise soil 1:1 (v/v) hygrometry=60% Temperature=24°C Light=200µmole photon .m-².s-1 (16h day / 8h night)

treatment_protocol: no treatment

tag: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001)


title: 22406.DR.1 (186.1)


title: 22111.HS.1 (199.1)


title: 22440.DR.1 (193.1)


title: 22287.HS.1 (185.1)


title: 14286411 - Col-0_BR2 vs Col-0::1390::MAS_BR2

hyb_protocol: Col-0::1390::MAS_BR2 Cy5 / Col-0_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286412 - Col-0::1390::MAS_BR2 vs Col-0_BR2

hyb_protocol: Col-0_BR2 Cy5 / Col-0::1390::MAS_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286409 - Col-0_BR1 vs Col-0::1390::MAS_BR1


title: 22281.HS.1 (179.1)


title: 14286408 - Col-0::1390::OCS_BR3 vs Col-0_BR3

hyb_protocol: Col-0_BR3 Cy5 / Col-0::1390::OCS_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 22111.C.1 (182.1)


title: 22293.DR.1 (183.1)


title: 22422.C.1 (178.1)


title: 22458.DR.1 (181.1)


title: 22299.HS.1 (18.1)


title: 22269.C.1 (177.1)


title: 22455.C.1 (184.1)


title: 22422.HS.1 (176.1)


title: 22440.HS.1 (175.1)


title: 14286403 - Col-0::1390::OCS_BR1 vs Col-0_BR1


title: 14286406 - Col-0::1390::OCS_BR2 vs Col-0_BR2

hyb_protocol: Col-0_BR2 Cy5 / Col-0::1390::OCS_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 22455.DR.1 (173.1)


title: 22458.HS.1 (172.1)


title: 22416.DR.1 (171.1)


title: 14286407 - Col-0_BR3 vs Col-0::1390::OCS_BR3

hyb_protocol: Col-0::1390::OCS_BR3 Cy5 / Col-0_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 22325.C.1 (17.1)


title: 14286402 - Col-0_BR1 vs Col-0::1390::OCS_BR1

hyb_protocol: Col-0::1390::OCS_BR1 Cy5 / Col-0_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286405 - Col-0_BR2 vs Col-0::1390::OCS_BR2

hyb_protocol: Col-0::1390::OCS_BR2 Cy5 / Col-0_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 22431.DR.1 (170.1)


title: 14286401 - Col-0::1390::MAS_BR3 vs Col-0_BR3

hyb_protocol: Col-0_BR3 Cy5 / Col-0::1390::MAS_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 22294.HS.1 (169.1)


title: 14286400 - Col-0_BR3 vs Col-0::1390::MAS_BR3

hyb_protocol: Col-0::1390::MAS_BR3 Cy5 / Col-0_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: [b] MPCCs_7day_tolcapone

city: Chicago

first: Brenton

middle: Robert

last: Ware

state: IL

address: 851 S Morgan St

department: Biomedical Engineering

institute: University of Illinois at Chicago

description:
Gene expression data from MPCCs treated with 4.51 µg/mL tolcapone for 7 days.
7day Tolcapone (III)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 microarray following manufacturer protocols.

scan_protocol: GeneChips were scanned using the Agilent Microarray Scanner BA.

data_processing: The data were normalized, modeled, and compared using the DNA Chip (dChip) Analyzer software.  Data from all chips were normalized to MPCCs treated with DMSO for 7 days (invariant set normalization).  Probe sets marked as 'present' on the 3T3-J2-only control chip were omitted from further analysis. Differentially expressed genes at each time-point were defined as those transcripts with |fold change| > 2.0 and |difference in expression| > 100 in drug-treated MPCCs relative to DMSO-only controls.

source_name: MPCCs treated with tolcapone for 7 days

label_protocol: Biotinylated cRNA was synthesized using the BioArray HighYield RNA Transcript Labeling Kit, purified over RNeasy columns (Qiagen), eluted, and then fragmented.

extract_protocol: Total RNA was extracted from cultures with the Rneasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: cell culture

value: MPCCs

tag: growth protocol

value: Plated cells

value: 4.51 µg/mL tolcapone

tag: duration

value: 7 days


title: 22299.C.1 (165.1)


title: 22419.HS.1 (168.1)


title: [b] MPCCs_7day_entacapone

description:
Gene expression data from MPCCs treated with 1.91 µg/mL entacapone for 7 days.
7day Entacapone (III)

source_name: MPCCs treated with entacapone for 7 days

value: 1.91 µg/mL entacapone


title: 22206.C.1 (164.1)


title: 22285.HS.1 (174.1)


title: 22361.C.1 (161.1)


title: 22343.DR.1 (163.1)


title: 22223.HS.1 (162.1)


title: 22245.C.1 (16.1)


title: [b] MPCCs_7day_ibufenac

description:
Gene expression data from MPCCs treated with 19.23 µg/mL ibufenac for 7 days.
7day Ibufenac (III)

source_name: MPCCs treated with ibufenac for 7 days

value: 19.23 µg/mL ibufenac


title: 22247.C.1 (160.1)


title: 22203.C.1 (159.1)


title: [b] MPCCs_7day_buspirone

description:
Gene expression data from MPCCs treated with 2.11 ng/mL buspirone for 7 days.
7day Buspirone (III)

source_name: MPCCs treated with buspirone for 7 days

value: 2.11 ng/mL buspirone


title: [b] MPCCs_7day_nefazodone

description:
Gene expression data from MPCCs treated with 434.55 ng/mL nefazodone for 7 days.
7day Nefazodone (III)

source_name: MPCCs treated with nefazodone for 7 days

value: 434.55 ng/mL nefazodone


title: 22320.DR.1 (167.1)


title: [b] MPCCs_7day_ibuprofen

description:
Gene expression data from MPCCs treated with 31.87 µg/mL ibuprofen for 7 days.
7day Ibuprofen (III)

source_name: MPCCs treated with ibuprofen for 7 days

value: 31.87 µg/mL ibuprofen


title: 22131.HS.1 (157.1)


title: 22319.HS.1 (158.1)


title: [b] MPCCs_7day_DMSO

description:
Gene expression data from MPCCs treated with 0.1% DMSO for 7 days.
7day DMSO (III)

source_name: MPCCs treated with DMSO for 7 days

value: 0.1% DMSO


title: 22263.DR.1 (154.1)

value: dietary restrictions


title: [b] 3T3-J2s_7day_troglitazone

description:
Gene expression data from pure 3T3-J2s treated with 2.82 µg/mL troglitazone for 7 days.
3T3-J2 (III)

source_name: 3T3-J2s treated with troglitazone for 7 days

value: 3T3-J2 fibroblasts

value: 2.82 µg/mL troglitazone


title: 22247.DR.1 (155.1)


title: 22205.DR.1 (152.1)


title: 22316.C.1 (153.1)

value: control


title: 22262.DR.1 (151.1)


title: 22205.C.1 (150.1)


title: 22349.C.1 (149.1)


title: 22307.C.1 (148.1)


title: 22131.DR.1 (147.1)


title: 22258.HS.1 (15.1)

value: high sugar


title: 22234.HS.1 (145.1)


title: 22149.DR.1 (156.1)


title: 22230.DR.1 (146.1)


title: 22311.C.1 (143.1)


title: 22320.HS.1 (140.1)


title: 22234.DR.1 (139.1)


title: 254706910095_b2 - S24_3days-after_induction_BR2 vs Ctrl24_3days-after_induction_BR2

description: Mitochondrial transcriptome regulation and coordination with the nucleus

hyb_protocol: Ctrl24_3days-after_induction_BR2 Cy5 / S24_3days-after_induction_BR2 Cy3 : 20pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 200 nmol.

growth_protocol: whole plant - Media=Agar plates with MS-255 medium, 1% w/v sucrose Temperature=24°C Light=Full dark

treatment_protocol: Name:Estradiol 3days - compound based treatment - compound addition,estradiol:quantity 185uM time 3day . Seedlings are grown on plates with 35 mL solid agar medium. Treatment is through addition of 2 mL liquid medium with 185 µM estradiol to each agar plate.

tag: arabidopsis thaliana (columbia)  mutant (col-0) -  dev.stage (boyes et al. plant cell 2001)


title: 22329.HS.1 (138.1)


title: 22381.C.1 (142.1)


title: 22305.C.1 (141.1)


title: 254706910083_b3 - Ctrl23_2days-after_induction_BR2 vs S23_2days-after_induction_BR2

hyb_protocol: S23_2days-after_induction_BR2 Cy5 / Ctrl23_2days-after_induction_BR2 Cy3 : 20pmol.

treatment_protocol: Name:Estradiol 2days - compound based treatment - compound addition,estradiol:quantity 185uM time 2day . Seedlings are grown on plates with 35 mL solid agar medium. Treatment is through addition of 2 mL liquid medium with 185 µM estradiol to each agar plate.


title: 22238.DR.1 (137.1)


title: 22177.HS.1 (136.1)


title: 254706910095_b3 - Ctrl25_4days-after_induction_BR2 vs S25_4days-after_induction_BR2

hyb_protocol: S25_4days-after_induction_BR2 Cy5 / Ctrl25_4days-after_induction_BR2 Cy3 : 20pmol.

treatment_protocol: Name:Estradiol 4days - compound based treatment - compound addition,estradiol:quantity 185uM time 4day . Seedlings are grown on plates with 35 mL solid agar medium. Treatment is through addition of 2 mL liquid medium with 185 µM estradiol to each agar plate.


title: 254706910082_b4 - S21_0day-after_induction_BR2 vs Ctrl21_0day-after_induction_BR2

hyb_protocol: Ctrl21_0day-after_induction_BR2 Cy5 / S21_0day-after_induction_BR2 Cy3 : 20pmol.


title: 254706910083_b1 - Ctrl22_1day-after_induction_BR2 vs S22_1day-after_induction_BR2

hyb_protocol: S22_1day-after_induction_BR2 Cy5 / Ctrl22_1day-after_induction_BR2 Cy3 : 20pmol.

treatment_protocol: Name:Estradiol 1day - compound based treatment - compound addition,estradiol:quantity 185uM time 1day . Seedlings are grown on plates with 35 mL solid agar medium. Treatment is through addition of 2 mL liquid medium with 185 µM estradiol to each agar plate.


title: 254706910083_b4 - S23_2days-after_induction_BR2 vs Ctrl23_2days-after_induction_BR2

hyb_protocol: Ctrl23_2days-after_induction_BR2 Cy5 / S23_2days-after_induction_BR2 Cy3 : 20pmol.


title: 254706910083_b2 - S22_1day-after_induction_BR2 vs Ctrl22_1day-after_induction_BR2

hyb_protocol: Ctrl22_1day-after_induction_BR2 Cy5 / S22_1day-after_induction_BR2 Cy3 : 20pmol.


title: 254706910095_b1 - Ctrl24_3days-after_induction_BR2 vs S24_3days-after_induction_BR2

hyb_protocol: S24_3days-after_induction_BR2 Cy5 / Ctrl24_3days-after_induction_BR2 Cy3 : 20pmol.


title: 22329.C.1 (135.1)


title: 254706910082_b3 - Ctrl21_0day-after_induction_BR2 vs S21_0day-after_induction_BR2

hyb_protocol: S21_0day-after_induction_BR2 Cy5 / Ctrl21_0day-after_induction_BR2 Cy3 : 20pmol.


title: 254706910095_b4 - S25_4days-after_induction_BR2 vs Ctrl25_4days-after_induction_BR2

hyb_protocol: Ctrl25_4days-after_induction_BR2 Cy5 / S25_4days-after_induction_BR2 Cy3 : 20pmol.


title: 22234.C.1 (144.1)


title: 254706910082_b2 - S20_4days-after_induction_BR1 vs Ctrl20_4days-after_induction_BR1

hyb_protocol: Ctrl20_4days-after_induction_BR1 Cy5 / S20_4days-after_induction_BR1 Cy3 : 20pmol.


title: 22249.DR.1 (133.1)


title: 22181.HS.1 (14.1)


title: 22325.HS.1 (131.1)


title: 22142.HS.1 (134.1)


title: 25_blastomere

type: genomic

city: Morristown

first: Nathan

middle: R

last: Treff

state: NJ

address: 111 Madison Ave

department: Molecular Biology

institute: RMA of NJ

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was digested with the NspI restriction enzyme, ligated to an adapter molecule, PCR amplified, fragmented with DNase I, labeled and hybridized to each array according to the manufacturer's instructions (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

scan_protocol: Each array was washed using Affymetrix fluidics station 640, and scanned using the Gene Chip Scanner 7G as recommended (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

data_processing: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls.  Copy number was calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual) analysis against a reference set of 30 normal females (published in GEO submission GSE24690) at a 5Mb Gaussian smoothing for aneuploid screening.

label: biotin

molecule: genomic DNA

source_name: cleavage stage embryo blastomere

label_protocol: Fragmented DNA was biotinylated using the manufacturers recommendations (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930)

extract_protocol: Biopsied polar body or blastomere and whole embryo samples underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).  Whole genome amplification was performed as previously described (Treff et al., 2010, Fertil. Steril., In Press).

tag: predicted karyotype


title: 26_blastomere

description: Hybridized to 250K_Nsp


title: 22370.HS.1 (130.1)


title: 22311.HS.1 (128.1)


title: 22263.HS.1 (129.1)


title: 24_blastomere

description: Hybridized to 250K_Nsp

value: nonconcurrent


title: 22315.DR.1 (132.1)

value: batch 1


title: 254706910081_b3 - Ctrl19_3days-after_induction_BR1 vs S19_3days-after_induction_BR1

hyb_protocol: S19_3days-after_induction_BR1 Cy5 / Ctrl19_3days-after_induction_BR1 Cy3 : 20pmol.


title: m1928z-3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: alloreactive ABM m1928z T cells

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

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

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

organism: Mus musculus

source_name: Sorted m1928z T cells from ABM --> BM12 spleen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: RPMI media with mouse IL2 and IL6, 37 degree 5% CO2 incubator

extract_protocol: RNA extraction plus kit was used to isolate RNA.

treatment_protocol: ABM mouse T cells were infected with retrovirus expressing m19delta and m1928z and adoptively transferred into B1M12 recipients of B6 BM,  GFP+ CAR cells were isolated by FACS.

tag: cell type

value: ABM mouseCAR T cells

tag: strain

tag: retrovirus


title: m1928z-2

description: alloreactive ABM m1928z T cells


title: 22320.C.1 (127.1)


title: 254706910081_b4 - S19_3days-after_induction_BR1 vs Ctrl19_3days-after_induction_BR1

hyb_protocol: Ctrl19_3days-after_induction_BR1 Cy5 / S19_3days-after_induction_BR1 Cy3 : 20pmol.


title: 254706910081_b1 - Ctrl18_2days-after_induction_BR1 vs S18_2days-after_induction_BR1

hyb_protocol: S18_2days-after_induction_BR1 Cy5 / Ctrl18_2days-after_induction_BR1 Cy3 : 20pmol.


title: m1928z-1

description: alloreactive ABM m1928z T cells


title: 254706910080_b3 - Ctrl17_1day-after_induction_BR1 vs S17_1day-after_induction_BR1

hyb_protocol: S17_1day-after_induction_BR1 Cy5 / Ctrl17_1day-after_induction_BR1 Cy3 : 20pmol.


title: m1928z-5

description: alloreactive ABM m1928z T cells


title: m1928z-4

description: alloreactive ABM m1928z T cells


title: m19delta-3

description: alloreactive ABM m19delta T cells

source_name: Sorted m19delta T cells from ABM --> BM12 spleen


title: 22300.HS.1 (126.1)


title: m19delta-2

description: alloreactive ABM m19delta T cells


title: 254706910081_b2 - S18_2days-after_induction_BR1 vs Ctrl18_2days-after_induction_BR1

hyb_protocol: Ctrl18_2days-after_induction_BR1 Cy5 / S18_2days-after_induction_BR1 Cy3 : 20pmol.


title: 254706910080_b4 - S17_1day-after_induction_BR1 vs Ctrl17_1day-after_induction_BR1

hyb_protocol: Ctrl17_1day-after_induction_BR1 Cy5 / S17_1day-after_induction_BR1 Cy3 : 20pmol.


title: 21_blastomere

description: Hybridized to 250K_Nsp


title: 22_blastomere

description: Hybridized to 250K_Nsp


title: 22343.HS.1 (13.1)


title: 22257.C.1 (125.1)


title: 254706910082_b1 - Ctrl20_4days-after_induction_BR1 vs S20_4days-after_induction_BR1

hyb_protocol: S20_4days-after_induction_BR1 Cy5 / Ctrl20_4days-after_induction_BR1 Cy3 : 20pmol.


title: m19delta-1

description: alloreactive ABM m19delta T cells


title: 23_blastomere

description: Hybridized to 250K_Nsp


title: 18_blastomere

description: Hybridized to 250K_Nsp


title: 254706910080_b2 - S16_0day-after_induction_BR1 vs Ctrl16_0day-after_induction_BR1

hyb_protocol: Ctrl16_0day-after_induction_BR1 Cy5 / S16_0day-after_induction_BR1 Cy3 : 20pmol.


title: 254706910080_b1 - Ctrl16_0day-after_induction_BR1 vs S16_0day-after_induction_BR1

hyb_protocol: S16_0day-after_induction_BR1 Cy5 / Ctrl16_0day-after_induction_BR1 Cy3 : 20pmol.


title: 22245.HS.1 (124.1)


title: 17_blastomere

description: Hybridized to 250K_Nsp


title: 16_blastomere

description: Hybridized to 250K_Nsp


title: 15_blastomere

description: Hybridized to 250K_Nsp


title: 49_whole embryo

description: Hybridized to 250K_Nsp

source_name: whole embryo


title: 22247.HS.1 (122.1)


title: 22310.C.1 (121.1)


title: 48_whole embryo

description: Hybridized to 250K_Nsp


title: 22259.HS.1 (12.1)


title: 47_polar body

description: Hybridized to 250K_Nsp

source_name: polar body

value: normal


title: 45_polar body

description: Hybridized to 250K_Nsp


title: 46_polar body

description: Hybridized to 250K_Nsp


title: 22259.C.1 (120.1)


title: 22206.DR.1 (119.1)


title: 22381.DR.1 (118.1)


title: 44_polar body

description: Hybridized to 250K_Nsp


title: 22304.C.1 (117.1)


title: 254706910112_b4 - myc4_BR2 vs ws_BR2

description: identification of new transcription factors for lignin biosynthesis

hyb_protocol: ws_BR2 Cy5 / myc4_BR2 Cy3 : 20pmol.

growth_protocol: stem - Media=soil hygrometry=relative humidity (60%) Temperature=22 ℃ day and 16 ℃ night, 150 μmol/m2 × s Light=16h light/ 8h dark

extract_protocol: ws_BR2:5ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (wassilewskija)  -  dev.stage (boyes et al. plant cell 2001)

extract_protocol: myc4_BR2:5ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (wassilewskija)  mutant (myc4 overexpressor) -  dev.stage (boyes et al. plant cell 2001)


title: 22230.HS.1 (116.1)


title: 254706910113_b2 - myc4_BR3 vs ws_BR3

hyb_protocol: ws_BR3 Cy5 / myc4_BR3 Cy3 : 20pmol.

extract_protocol: ws_BR3:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: myc4_BR3:5ug. (Qiagen_RNeasy.pdf)


title: 22306.C.1 (114.1)


title: 254706910112_b1 - ws_BR1 vs myc4_BR1

hyb_protocol: myc4_BR1 Cy5 / ws_BR1 Cy3 : 20pmol.

extract_protocol: myc4_BR1:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: ws_BR1:5ug. (Qiagen_RNeasy.pdf)


title: 254706910112_b2 - myc4_BR1 vs ws_BR1

hyb_protocol: ws_BR1 Cy5 / myc4_BR1 Cy3 : 20pmol.


title: 254706910079_b1 - Col0_0h_BR1 vs Col0_24h_BR1

description: Effect of a mixture of molecules stemming from industrial process

hyb_protocol: Col0_24h_BR1 Cy5 / Col0_0h_BR1 Cy3 : 20pmol.

growth_protocol: cell culture/primary cell - Suspension cells are maintained at 22°c continuous light in Gamborg medium

extract_protocol: Col0_24h_BR1:2ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:culture_residue_1h - time course study - compound addition,mixture from industrial partner:time 1hour . Suspension cells are maintained at 22°c continuous light in Gamborg medium. Suspension cells were used 7 days after subculture. At day of treatments cells were submit to treatment (1% (v/v) mixture given by industrial partner). Cells were harvested with no treatment (control) and 1 or 4 or 24 hr after treatment.

tag: arabidopsis thaliana (columbia)  - age

extract_protocol: Col0_0h_BR1:2ug. (Qiagen_RNeasy.pdf)


title: 254706910079_b2 - Col0_24h_BR1 vs Col0_0h_BR1

hyb_protocol: Col0_0h_BR1 Cy5 / Col0_24h_BR1 Cy3 : 20pmol.


title: 254706910076_b4 - Col0_4h_BR2 vs Col0_0h_BR2

hyb_protocol: Col0_0h_BR2 Cy5 / Col0_4h_BR2 Cy3 : 20pmol.

extract_protocol: Col0_0h_BR2:2ug. (Qiagen_RNeasy.pdf)

extract_protocol: Col0_4h_BR2:2ug. (Qiagen_RNeasy.pdf)


title: ASM9

city: Beijing

first: Yuguang

last: Zhang

address: Haidian

country: China

institute: Chinese Academy of Forestry

description: GeoChip data for soil sample collected in Qinghai-Tibetan, replicate 9

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes.The hybridization was carried out at 42 for 16 hours on a hybrization station (Qiagen, Valencia, CA, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv)  remove genes detected in at least two out of ten samples from the same site.

organism: uncultured soil microorganism

source_name: soil sample collected from alpine-steppe meadow in Qinghai-Tibetan

label_protocol: As previously described (Qingyun Yan et al 2013), DNA samples were labeled with the fluorescent dye Cy3 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA) and then dried in a SpeedVac (Thermo Savant, NY, USA).

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

treatment_protocol: In July, 2012, soil samples were collected from the plots. Five to ten soil cores at a depth of 0-10 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

tag: collected from

value: meadow steppe alpine soil

tag: latitudes


title: 254706910113_b1 - ws_BR3 vs myc4_BR3

hyb_protocol: myc4_BR3 Cy5 / ws_BR3 Cy3 : 20pmol.


title: ASM10

description: GeoChip data for soil sample collected in Qinghai-Tibetan, replicate 10


title: 254706910079_b4 - Col0_24h_BR2 vs Col0_0h_BR2

hyb_protocol: Col0_0h_BR2 Cy5 / Col0_24h_BR2 Cy3 : 20pmol.

extract_protocol: Col0_24h_BR2:2ug. (Qiagen_RNeasy.pdf)


title: 254706910076_b3 - Col0_0h_BR2 vs Col0_4h_BR2

hyb_protocol: Col0_4h_BR2 Cy5 / Col0_0h_BR2 Cy3 : 20pmol.


title: 254706910079_b3 - Col0_0h_BR2 vs Col0_24h_BR2

hyb_protocol: Col0_24h_BR2 Cy5 / Col0_0h_BR2 Cy3 : 20pmol.


title: 22298.DR.1 (111.1)

source_name: whole fly

extract_protocol: Trizol extraction followed by a Qiagen clean up

tag: recombinant inbred line

tag: treatment

tag: batch


title: 22203.HS.1 (112.1)


title: 22304.DR.1 (110.1)


title: ASM7

description: GeoChip data for soil sample collected in Qinghai-Tibetan, replicate 7


title: 22213.DR.1 (115.1)


title: ASM6

description: GeoChip data for soil sample collected in Qinghai-Tibetan, replicate 6


title: ASM5

description: GeoChip data for soil sample collected in Qinghai-Tibetan, replicate 5


title: 22184.HS.1 (113.1)


title: 254706910076_b1 - Col0_0h_BR1 vs Col0_4h_BR1

hyb_protocol: Col0_4h_BR1 Cy5 / Col0_0h_BR1 Cy3 : 20pmol.

extract_protocol: Col0_4h_BR1:2ug. (Qiagen_RNeasy.pdf)


title: 254706910076_b2 - Col0_4h_BR1 vs Col0_0h_BR1

hyb_protocol: Col0_0h_BR1 Cy5 / Col0_4h_BR1 Cy3 : 20pmol.


title: ASM8

description: GeoChip data for soil sample collected in Qinghai-Tibetan, replicate 8


title: 22366.DR.1 (109.1)


title: 22326.C.1 (11.1)


title: 22339.C.1 (107.1)


title: ASM4

description: GeoChip data for soil sample collected in Qinghai-Tibetan, replicate 4


title: 254706910075_b4 - Col0_1h_BR2 vs Col0_0h_BR2

hyb_protocol: Col0_0h_BR2 Cy5 / Col0_1h_BR2 Cy3 : 20pmol.

extract_protocol: Col0_1h_BR2:2ug. (Qiagen_RNeasy.pdf)


title: AM10

value: meadow apline soil


title: 22245.DR.1 (105.1)


title: 22379.HS.1 (108.1)


title: Flower bud_rep1

hyb_protocol: For 8x60k Array (RNA samples)  : The samples were hybridized onto array chickpea 8x60k (AMADID 37094). The hybridization was carried out at 65°C for 16 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 1 minute and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37o C for 1 minute

scan_protocol: The microarray slide was scanned using Agilent Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: Images were quantified using Feature Extraction Software ( Agilent) and raw data was obtained.

organism: Cicer arietinum

source_name: Mature plant

label_protocol: For 8x60k Array (RNA samples)  : The sample labeling was performed using Quick-Amp Labeling Kit, One Color (Agilent Technologies, Part Number: 5190-0442). 500ng of total RNA was denatured along with appropriate diluted Spike In controls; Spike A Mix/cyanine 3-CTP (Agilent Technologies, RNA Spike In Kit, One Color, Part Number 5188-5282) and oligo dT primer tagged to T7 promoter region primer at 65°C for 10 min followed by snap chilling on ice for 5 minutes. The cDNA master mix was added to the denatured RNA sample and incubated at 40°C for 2 hours. The cDNA sample was incubated at 65°C for 15 min in order to denature the enzymes. The in vitro transcription master mix was added to the cDNA sample and incubated at 40°C for 3 hours. The cDNA was in vitro transcribed into cRNA in presence of Cyanine 3-CTPdye. The Cyanine 3-CTP labeled cRNA sample was purified using Qiagen RNeasy column (Qiagen, Cat No: 74106). The concentrations of cRNA and dye incorporation were determined using Nanodrop-1000 (JH Bio).

growth_protocol: Chickpea seeds were grown in a culture room in mixture of agropeat and vermiculite or in the field. Root and shoot tissues were collected from 15-d-old seedlings and young pod and flower buds were collected from the field-grown plants.

extract_protocol: Total RNA was extarcted using TRI reagent from Sigma Life Science.

tag: tissue

value: Mature plant


title: 254706910075_b2 - Col0_1h_BR1 vs Col0_0h_BR1

hyb_protocol: Col0_0h_BR1 Cy5 / Col0_1h_BR1 Cy3 : 20pmol.

extract_protocol: Col0_1h_BR1:2ug. (Qiagen_RNeasy.pdf)


title: 254706910075_b1 - Col0_0h_BR1 vs Col0_1h_BR1

hyb_protocol: Col0_1h_BR1 Cy5 / Col0_0h_BR1 Cy3 : 20pmol.


title: AM9

source_name: soil sample collected from alpine meadow in Qinghai-Tibetan


title: Root_rep2

source_name: Seedling

value: 15-d-old seedling


title: Shoot_rep2


title: ASM2

description: GeoChip data for soil sample collected in Qinghai-Tibetan, replicate 2


title: 254706910053_b4 - sid2_BR2 vs pi4kbeta1beta2sid2_BR2

description: What are the transcriptome changes induced in the pi4kbeta1beta2 sid2 triple mutant ?

hyb_protocol: pi4kbeta1beta2sid2_BR2 Cy5 / sid2_BR2 Cy3 : 20pmol.

growth_protocol: rosette - Media=soil hygrometry=70% Temperature=22°C Light=long day

tag: arabidopsis thaliana (columbia)  mutant (col0) -  dev.stage (boyes et al. plant cell 2001)

extract_protocol: sid2_BR2:10ug. (Qiagen_RNeasy.pdf)


title: Flower bud_rep2


title: Young pod_rep2


title: Root_rep1


title: ASM3

description: GeoChip data for soil sample collected in Qinghai-Tibetan, replicate 3


title: ASM1

description: GeoChip data for soil sample collected in Qinghai-Tibetan, replicate 1


title: AM8


title: 22378.DR.1 (104.1)


title: 254706910053_b3 - pi4kbeta1beta2sid2_BR2 vs sid2_BR2

hyb_protocol: sid2_BR2 Cy5 / pi4kbeta1beta2sid2_BR2 Cy3 : 20pmol.


title: 254706910053_b2 - sid2_BR1 vs pi4kbeta1beta2sid2_BR1

hyb_protocol: pi4kbeta1beta2sid2_BR1 Cy5 / sid2_BR1 Cy3 : 20pmol.

extract_protocol: sid2_BR1:10ug. (Qiagen_RNeasy.pdf)


title: 254706910052_b4 - pi4kbeta1beta2sid2_BR2 vs pi4kbeta1beta2_BR2

hyb_protocol: pi4kbeta1beta2_BR2 Cy5 / pi4kbeta1beta2sid2_BR2 Cy3 : 20pmol.


title: Young pod_rep1


title: 254706910053_b1 - pi4kbeta1beta2sid2_BR1 vs sid2_BR1

hyb_protocol: sid2_BR1 Cy5 / pi4kbeta1beta2sid2_BR1 Cy3 : 20pmol.


title: Shoot_rep1


title: 254706910075_b3 - Col0_0h_BR2 vs Col0_1h_BR2

hyb_protocol: Col0_1h_BR2 Cy5 / Col0_0h_BR2 Cy3 : 20pmol.


title: AM7

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes.The hybridization was carried out at 42 for 16 hours on a hybrization station (Qiagen, Valencia, CA, USA).


title: 22262.C.1 (103.1)


title: 22167.C.1 (123.1)


title: 22316.DR.1 (101.1)


title: 22378.C.1 (100.1)


title: rta3 mutant-3

description: mutant untreated

hyb_protocol: Samples that pass the QC for specific activity were taken for hybridization. 1000ng of labeled cRNA were hybridized on the array (AMADID: 26377) using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent).

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Images were quantified using Feature Extraction software Version 11.5.1.1 of Agilent. Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Candida albicans

source_name: rta3 mutant

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using primer mix of random hexamer and oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: The wild type and mutant were grown in Yeast Peptone Glucose (2%) till log phase at 30°C/220 rpm shaking

extract_protocol: RNA isolation was performed by using  Qiagen RNeasy mini kit (Cat # 74106) following the manufacturer's recommendations.

tag: genotype/variation

value: rta3 mutant


title: SC5314-3

description: Wild type C.albicans strain

value: Wild type


title: AM6


title: 22167.HS.1 (102.1)


title: 22138.DR.1 (10.1)


title: rta3 mutant-2

description: mutant untreated


title: SC5314-2

description: Wild type C.albicans strain


title: rta3 mutant-1

description: mutant untreated


title: AM5


title: AM4


title: AM3


title: 254706910052_b2 - pi4kbeta1beta2sid2_BR1 vs pi4kbeta1beta2_BR1

hyb_protocol: pi4kbeta1beta2_BR1 Cy5 / pi4kbeta1beta2sid2_BR1 Cy3 : 20pmol.


title: 254706910052_b3 - pi4kbeta1beta2_BR2 vs pi4kbeta1beta2sid2_BR2

hyb_protocol: pi4kbeta1beta2sid2_BR2 Cy5 / pi4kbeta1beta2_BR2 Cy3 : 20pmol.


title: AM2


title: SC5314-1

description: Wild type C.albicans strain


title: 254706910051_b3 - col0_BR2 vs pi4kbeta1beta2_BR2

hyb_protocol: pi4kbeta1beta2_BR2 Cy5 / col0_BR2 Cy3 : 20pmol.

extract_protocol: col0_BR2:10ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001)


title: 254706910051_b2 - pi4kbeta1beta2_BR1 vs col0_BR1

hyb_protocol: col0_BR1 Cy5 / pi4kbeta1beta2_BR1 Cy3 : 20pmol.

extract_protocol: col0_BR1:10ug. (Qiagen_RNeasy.pdf)


title: 254706910112_b3 - ws_BR2 vs myc4_BR2

hyb_protocol: myc4_BR2 Cy5 / ws_BR2 Cy3 : 20pmol.

extract_protocol: myc4_BR2:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: ws_BR2:5ug. (Qiagen_RNeasy.pdf)


title: AM1


title: 22350.HS.1 (1.1)


title: adult,female,whole-body,Bateman (chip E)

status: Public on Jan 04 2017

city: St Lucia

first: Stephen

last: Chenoweth

state: QLD

address: The School of Biological Sciences, The University of Queensland

country: Australia

institute: The University of Queensland, Australia

description:
adult,female,whole-body,Bateman
chip_E_array_9_Bateman_F

hyb_protocol: Hybridization was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following standard NimbleGen operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following standard NimbleGen operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was normalized via a log (base 2) tranformation. Summarisation was performed by first taking the mean of replicated probes followed by the median of a probe set.

organism: Drosophila serrata

source_name: adult, female, whole-body, Bateman

label_protocol: Labeling was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following standard NimbleGen operating protocol. See www.nimblegen.com.

growth_protocol: All flies were reared in 50ml vials containing standard yeast medium at 25°C with a 12 hour day/night cycle and adult flies were held in vials for three days in same sex groups of 5 before being frozen. The samples were snap frozen in liquid nitrogen without the use of CO2 anesthesia. Freezing began at 10:22 am and was completed by 1:40 pm. All flies were frozen in a random order with respect to sex and population.

extract_protocol: Each whole-body pool was homogenized in Trizol® following snap freezing of tissue and then immediately stored at -80 degrees Celcius. RNA extraction of the whole-body samples was performed by using the Trizol® procedure followed by RNA isolation using RNeasy minikits®.

tag: Sex

value: female

tag: population

value: Bateman

tag: latitude

value: whole body


title: 254706910051_b4 - pi4kbeta1beta2_BR2 vs col0_BR2

hyb_protocol: col0_BR2 Cy5 / pi4kbeta1beta2_BR2 Cy3 : 20pmol.


title: MCA-OVA-bearing mice treated with control Ab #4

city: Kyoto

first: Hirotake

last: Tsukamoto

state: Sakyo-Ku

address: 53 Kawahara-cho Shogoin

department: Center for Cancer Immunotherapy and Immunobiology

country: Japan

institute: Kyoto University

description: Gene expression in CD4+ T cells from tumor-bearing, control Ab-treated mice

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >14.0 pmol Cy3/ug cDNA) was fragmented at 60 °C for 30 minutes, and were hybridized to SurePrint G3 Mouse GE microarray 8X60K v2 Microarrays Kit (G4853B) using Gene Expression Hybridization Kit (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting  (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software Version 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Raw fluorescent data was extracted using GeneSpring GX software 14.5.0 (Agilent), were then subjected to log2 transformation and 75th percentile normalization for analysis.

source_name: isolated CD4 T cells #4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit and Agilent RNA Spike-In Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from CD4+ T cells using the TRIZOL Reagent (Thermo Fisher Scientific), followed by the further purification via RNeasy mini columes (QIAGEN).  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C57BL/6 mice were inculated with ovalbumin(OVA)-expressing MCA205 fibrosarcoma, and then were transferred with OVA-specific TCR transgenic CD4+ T cells. Furthermore, those mice were immunized by the transfer of OVA peptide-pulsed dendritic cells with or without simultaneous injection of anti-IL-6R Ab. The same treatments were also conducted in tumor-free mice. Four days after in vivo immunization, CD4+ T cells were isolated from those mice (four groups). The total RNA isolated from those CD4+ T cells were utilized for microarray analysis.

tag: strain

tag: host

value: MCA-OVA-bearing mice

value: control Ab

tag: cell type

value: CD4+ T cell


title: adult,male,whole-body,Bateman (chip E)

description:
adult,male,whole-body,Bateman
chip_E_array_2_Bateman_M

source_name: adult, male, whole-body, Bateman

value: male


title: tumor-free mice treated with control Ab #1

description: Gene expression in CD4+ T cells from tumor-free, control Ab-treated mice

source_name: isolated CD4 T cells #1

value: tumor-free mice


title: MCA-OVA-bearing mice treated with control Ab #3

source_name: isolated CD4 T cells #3


title: adult,male,whole-body,Forster (chip E)

description:
adult,male,whole-body,Forster
chip_E_array_12_Forster_M

source_name: adult, male, whole-body, Forster

value: Forster


title: adult,female,whole-body,CoffsH (chip E)

description:
adult,female,whole-body,CoffsH
chip_E_array_5_CoffsH_F

source_name: adult, female, whole-body, CoffsH


title: MCA-OVA-bearing mice treated with anti-IL-6R Ab  #8

description: Gene expression in CD4+ T cells from tumor-bearing, anti-IL-6R Ab-treated mice

source_name: isolated CD4 T cells #8

value: anti-IL-6R Ab


title: adult,male,whole-body,Terrigal (chip E)

description:
adult,male,whole-body,Terrigal
chip_E_array_7_Terrigal_M

source_name: adult, male, whole-body, Terrigal

value: Terriga


title: adult,female,whole-body,Brisbane (chip E)

description:
adult,female,whole-body,Brisbane
chip_E_array_8_Brisbane_F

source_name: adult, female, whole-body, Brisbane

value: Brisban


title: adult,female,whole-body,Forster (chip E)

description:
adult,female,whole-body,Forster
chip_E_array_10_Forster_F

source_name: adult, female, whole-body, Forster


title: tumor-free mice treated with anti-IL-6R Ab #6

description: Gene expression in CD4+ T cells from tumor-free, anti-IL-6R Ab-treated mice

source_name: isolated CD4 T cells #6


title: adult,male,whole-body,CoffsH (chip E)

description:
adult,male,whole-body,CoffsH
chip_E_array_3_CoffsH_M

source_name: adult, male, whole-body, CoffsH


title: adult,female,whole-body,Airlie (chip E)

description:
adult,female,whole-body,Airlie
chip_E_array_6_Airlie_F

source_name: adult, female, whole-body, Airlie

value: Airlie


title: adult,female,whole-body,Cooktown (chip E)

description:
adult,female,whole-body,Cooktown
chip_E_array_1_Cooktown_F

source_name: adult, female, whole-body, Cooktown

value: Cooktow


title: tumor-free mice treated with control Ab #2

source_name: isolated CD4 T cells #2


title: 254706910051_b1 - col0_BR1 vs pi4kbeta1beta2_BR1

description: What are the transcriptome changes induced in the pi4kbeta1beta2 sid2 triple mutant ?

hyb_protocol: pi4kbeta1beta2_BR1 Cy5 / col0_BR1 Cy3 : 20pmol.


title: MCA-OVA-bearing mice treated with anti-IL-6R Ab  #7

source_name: isolated CD4 T cells #7


title: tumor-free mice treated with anti-IL-6R Ab #5

source_name: isolated CD4 T cells #5


title: adult,male,whole-body,Terrigal (chip D)

description:
adult,male,whole-body,Terrigal
chip_D_array_4_Terrigal_M


title: adult,female,whole-body,Brisbane (chip D)

description:
adult,female,whole-body,Brisbane
chip_D_array_6_Brisbane_F


title: adult,male,whole-body,Cooktown (chip E)

description:
adult,male,whole-body,Cooktown
chip_E_array_4_Cooktown_M

source_name: adult, male, whole-body, Cooktown


title: adult,male,whole-body,Yeppoon (chip D)

description:
adult,male,whole-body,Yeppoon
chip_D_array_3_Yeppoon_M

source_name: adult, male, whole-body, Yeppoon

value: Yeppoon


title: adult,male,whole-body,Cooktow (chip D)

description:
adult,male,whole-body,Cooktow
chip_D_array_12_Cooktow_M

source_name: adult, male, whole-body, Cooktow


title: adult,female,whole-body,Forster (chip D)

description:
adult,female,whole-body,Forster
chip_D_array_2_Forster_F


title: adult,female,whole-body,Terrigal (chip D)

description:
adult,female,whole-body,Terrigal
chip_D_array_9_Terrigal_F

source_name: adult, female, whole-body, Terrigal


title: adult,female,whole-body,Bateman (chip D)

description:
adult,female,whole-body,Bateman
chip_D_array_10_Bateman_F

source_name: adult, female, whole-body, Bateman


title: adult,male,whole-body,Brisbane (chip C)

description:
adult,male,whole-body,Brisbane
chip_C_array_8_Brisbane_M

source_name: adult, male, whole-body, Brisbane


title: adult,female,whole-body,Terrigal (chip C)

description:
adult,female,whole-body,Terrigal
chip_C_array_9_Terrigal_F


title: adult,male,whole-body,Forster (chip C)

description:
adult,male,whole-body,Forster
chip_C_array_5_Forster_M

source_name: adult, male, whole-body, Forster


title: adult,male,whole-body,Bateman (chip D)

description:
adult,male,whole-body,Bateman
chip_D_array_11_Bateman_M

source_name: adult, male, whole-body, Bateman


title: adult,female,whole-body,CoffsH (chip D)

description:
adult,female,whole-body,CoffsH
chip_D_array_1_CoffsH_F

source_name: adult, female, whole-body, CoffsH


title: adult,female,whole-body,CoffsH (chip C)

description:
adult,female,whole-body,CoffsH
chip_C_array_3_CoffsH_F


title: adult,male,whole-body,Terrigal (chip C)

description:
adult,male,whole-body,Terrigal
chip_C_array_4_Terrigal_M

source_name: adult, male, whole-body, Terrigal


title: adult,female,whole-body,Forster (chip B)

description:
adult,female,whole-body,Forster
chip_B_array_9_Forster_F

source_name: adult, female, whole-body, Forster


title: adult,male,whole-body,CoffsH (chip C)

description:
adult,male,whole-body,CoffsH
chip_C_array_6_CoffsH_M

source_name: adult, male, whole-body, CoffsH


title: adult,male,whole-body,Airlie (chip B)

description:
adult,male,whole-body,Airlie
chip_B_array_6_Airlie_M

source_name: adult, male, whole-body, Airlie


title: adult,female,whole-body,Yeppoon (chip B)

description:
adult,female,whole-body,Yeppoon
chip_B_array_7_Yeppoon_F

source_name: adult, female, whole-body, Yeppoon


title: adult,female,whole-body,Yeppoon (chip C)

description:
adult,female,whole-body,Yeppoon
chip_C_array_11_Yeppoon_F


title: adult,male,whole-body,Airlie (chip C)

description:
adult,male,whole-body,Airlie
chip_C_array_2_Airlie_M


title: adult,female,whole-body,Bateman (chip C)

description:
adult,female,whole-body,Bateman
chip_C_array_1_Bateman_F


title: adult,male,whole-body,Yeppoon (chip B)

description:
adult,male,whole-body,Yeppoon
chip_B_array_1_Yeppoon_M


title: adult,male,whole-body,Brisbane (chip B)

description:
adult,male,whole-body,Brisbane
chip_B_array_4_Brisbane_M


title: adult,female,whole-body,Yeppoon (chip A)

description:
adult,female,whole-body,Yeppoon
chip_A_array_9_Yeppoon_F


title: adult,female,whole-body,Airlie (chip A)

description:
adult,female,whole-body,Airlie
chip_A_array_7_Airlie_F

source_name: adult, female, whole-body, Airlie


title: adult,female,whole-body,Brisbane (chip A)

description:
adult,female,whole-body,Brisbane
chip_A_array_11_Brisbane_F

source_name: adult, female, whole-body, Brisbane


title: adult,male,whole-body,Bateman (chip A)

description:
adult,male,whole-body,Bateman
chip_A_array_6_Bateman_M


title: adult,female,whole-body,Airlie (chip B)

description:
adult,female,whole-body,Airlie
chip_B_array_3_Airlie_F


title: adult,male,whole-body,CoffsH (chip B)

description:
adult,male,whole-body,CoffsH
chip_B_array_8_CoffsH_M


title: adult,male,whole-body,Brisbane (chip A)

description:
adult,male,whole-body,Brisbane
chip_A_array_3_Brisbane_M


title: adult,female,whole-body,Cooktown (chip B)

description:
adult,female,whole-body,Cooktown
chip_B_array_5_Cooktown_F

source_name: adult, female, whole-body, Cooktown


title: adult,female,whole-body,Terrigal (chip B)

description:
adult,female,whole-body,Terrigal
chip_B_array_12_Terrigal_F


title: 22307.HS.1 (106.1)

source_name: whole fly

value: high sugar

value: batch 1


title: adult,male,whole-body,Airlie (chip A)

description:
adult,male,whole-body,Airlie
chip_A_array_10_Airlie_M


title: adult,male,whole-body,Yeppoon (chip A)

description:
adult,male,whole-body,Yeppoon
chip_A_array_1_Yeppoon_M

source_name: adult, male, whole-body, Yeppoon


title: adult,female,whole-body,Cooktown (chip A)

description:
adult,female,whole-body,Cooktown
chip_A_array_12_Cooktown_F

value: female


title: Pparβ/δ-/-_Ethanol_3

city: University Park

first: Pei-Li

last: Yao

address: 312 Life Sciences Building

institute: Pennsylvania State University

hyb_protocol: Prepare hybridization cocktail using the GeneChip Hybridization Wash and Stain Kit (#702232) and hybridize arrays according to the manufacturer’s instructions in the Affymetrix GeneChip Hybridization Oven 640. Following hybridization; wash and stain arrays using the Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’s protocol using the GeneChip Hybridization Wash and Stain Kit (#702232)

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

data_processing: Data was normalized using the Robust Multichip Average (RMA) approach as previously described (Do and Choi, 2006) .

label_protocol: Using 100 ng of total RNA from each sample, generate second-cycle single stranded sense strand cDNA using the Ambion WT Expression Kit (#4411974). Fragment the sense strand cDNA according to the manufacturer’s instructions using the Affymetrix GeneChip WT Terminal Labeling Kit (#900671) and confirm proper fragmentation using an RNA Nano Chip on the Agilent Bioanalyzer.Label the resulting fragmented cDNA using the Affymetrix GeneChip WT Terminal Labeling Kit (#900671) according to the manufacturer’s protocol. Assess labeling efficiency with the gel shift assay described by the manufacturer but utilizing an Agilent Bioanalyzer RNA Nano Chip instead of PAGE.

growth_protocol: Male wild-type or Pparβ/δ-null mice on a C57BL/6 genetic background were housed in a temperature controlled environment (25 °C) with a 12-h light/dark cycle.

extract_protocol: Total RNA were extracted using Rneasy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Mice were fed with the control diet for one week to acclimate to the liquid diet and then fed with either the control or ethanol liquid diet (4% v/v) for sixteen weeks..

tag: strain background

tag: age

value: 8-10 weeks

tag: gender

tag: strain info.

value: Pparβ/δ-/-

tag: fed with

value: ethanol diet for 16wks

value: Liver


title: Pparβ/δ-/-_Ethanol_2


title: Wild-type_Ethanol_3

value: Wild-type


title: Pparβ/δ-/-_Control_1

value: male

value: liquid control diet for 16wks


title: Wild-type_Control_1


title: Pparβ/δ-/-_Control_2


title: Wild-type_Ethanol_1


title: Wild-type_Ethanol_2


title: Pparβ/δ-/-_Ethanol_1


title: Wild-type_Control_2


title: HV-004-0

hyb_protocol: Labeled  RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 1.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 640. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

source_name: Healthy volunteer #4

growth_protocol: not applicable

extract_protocol: PaxGene microRNA Isolation kit

value: Male

tag: race

value: White

value: Whole venous blood


title: HV-010-0

source_name: Healthy volunteer #10

value: Female


title: AIS-002-1

source_name: Acutely injured subject #2 day 1


title: AIS-001-0

source_name: Acutely injured subject #1 Day 0


title: HV-009-0

source_name: Healthy volunteer #9


title: Pparβ/δ-/-_Control_3


title: AIS-002-0

source_name: Acutely injured subject #2 Day 0


title: AIS-001-2

source_name: Acutely injured subject #1 Day 2


title: AIS-002-4

source_name: Acutely injured subject #2 day 4


title: AIS-002-2

source_name: Acutely injured subject #2 day 2


title: AIS-001-1

source_name: Acutely injured subject #1 Day 1


title: AIS-002-3

source_name: Acutely injured subject #2 day 3


title: HV-018-0

source_name: Healthy volunteer #18


title: HV-002-0

source_name: Healthy volunteer #2


title: Wild-type_Control_3


title: 254706910052_b1 - pi4kbeta1beta2_BR1 vs pi4kbeta1beta2sid2_BR1

description: What are the transcriptome changes induced in the pi4kbeta1beta2 sid2 triple mutant ?

hyb_protocol: pi4kbeta1beta2sid2_BR1 Cy5 / pi4kbeta1beta2_BR1 Cy3 : 20pmol.


title: glomeruli_FSGS_repM4

city: Shanghai

first: Jun

last: Tong

state: Shanghai

address: 197,Ruijin Er Road

department: Nephrology

institute: Shanghai Jiaotong University

hyb_protocol: Total RNA was converted into cDNA, which was fragmented, labeled, and hybridized onto gene chips (Microarray Gene 1.0, Affymetrix, Santa Clara, CA) according to Affymetrix standard protocols.

scan_protocol: Affymetrix® Expression Console Software (version 1.2.1) was used for microarray analyses.

data_processing: Robust Multichip Average (RMA) was used with the default configuration for background adjustment and normalization. LIMMA was used using a q-value < 5% for the identification of differentially expressed genes in microarray experiments in R. The threshold was set to P <0.005 for LIMMA and fold-change > 1.5.

source_name: kidney

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

extract_protocol: glomeruli were isolated under an inverted microscope

treatment_protocol: Patients involved in our study were clinically manifested with newly diagnosed nephrotic syndrome without previous use of glucocorticoids or immunosuppressants at the point of receiving renal biopsy

value: glomeruli isolated from kidney

tag: disease state

value: MCD


title: glomeruli_FSGS_repM5

tag: tissue


title: glomeruli_FSGS_repM1


title: glomeruli_FSGS_repM2


title: glomeruli_FSGS_repM3


title: glomeruli_FSGS_repF5

value: FSGS


title: glomeruli_FSGS_repF2


title: glomeruli_FSGS_repF1


title: glomeruli_FSGS_repF3


title: glomeruli_FSGS_repF4


title: glomeruli_FSGS_repF6


title: adult,male,whole-body,Forster (chip D)

description:
adult,male,whole-body,Forster
chip_D_array_5_Forster_M

source_name: adult, male, whole-body, Forster

value: Forster

value: whole body


title: genomic DNA from skin peri-umbilical punch biopsy 304

city: London

first: Tim

last: Spector

address: Westminster Bridge road

department: Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Beadchips were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The Intensity Data files (*.txt) from GenomeStudio were uploaded into R (version 3.1.1). The methylation values were calculated as: beta = methylated signal/(methylated signal + unmethylated signal + 100). Further data quality control was all performed in R. Probes were removed that: 1) failed detection (p > 0.01) in one or more samples and/or had a bead count less than 3 in more than 5% of samples (n = 3,325), 2) aligned to more than one location in the human genome with their 50 bp sequence, 3) located on the sex chromosomes. This data set includes probes with genetic variants as used for part of the analysis in manuscript.

label: Cy5 and Cy3

source_name: skin peri-umbilical punch biopsy 304

label_protocol: Cy5 and Cy3

extract_protocol: Genomic DNA was extracted and purified from peripheral blood samples

value: skin

tag: beadchip and order on beadchip (sentrix id)

tag: age at biopsy

value: female

tag: relatedness identification id

tag: age at total body naevus count

tag: total body naevus count

tag: bisulphite conversion average

tag: bmi

tag: smoking status


title: genomic DNA from skin peri-umbilical punch biopsy 301

source_name: skin peri-umbilical punch biopsy 301


title: genomic DNA from skin peri-umbilical punch biopsy 313

source_name: skin peri-umbilical punch biopsy 313


title: genomic DNA from skin peri-umbilical punch biopsy 302

source_name: skin peri-umbilical punch biopsy 302


title: genomic DNA from skin peri-umbilical punch biopsy 310

source_name: skin peri-umbilical punch biopsy 310


title: genomic DNA from skin peri-umbilical punch biopsy 311

source_name: skin peri-umbilical punch biopsy 311


title: genomic DNA from skin peri-umbilical punch biopsy 316

source_name: skin peri-umbilical punch biopsy 316


title: genomic DNA from skin peri-umbilical punch biopsy 312

source_name: skin peri-umbilical punch biopsy 312


title: genomic DNA from skin peri-umbilical punch biopsy 306

source_name: skin peri-umbilical punch biopsy 306


title: genomic DNA from skin peri-umbilical punch biopsy 322

source_name: skin peri-umbilical punch biopsy 322


title: genomic DNA from skin peri-umbilical punch biopsy 315

source_name: skin peri-umbilical punch biopsy 315


title: genomic DNA from skin peri-umbilical punch biopsy 308

source_name: skin peri-umbilical punch biopsy 308


title: genomic DNA from skin peri-umbilical punch biopsy 305

source_name: skin peri-umbilical punch biopsy 305


title: genomic DNA from skin peri-umbilical punch biopsy 294

source_name: skin peri-umbilical punch biopsy 294


title: genomic DNA from skin peri-umbilical punch biopsy 300

source_name: skin peri-umbilical punch biopsy 300


title: genomic DNA from skin peri-umbilical punch biopsy 319

source_name: skin peri-umbilical punch biopsy 319


title: genomic DNA from skin peri-umbilical punch biopsy 296

source_name: skin peri-umbilical punch biopsy 296


title: genomic DNA from skin peri-umbilical punch biopsy 309

source_name: skin peri-umbilical punch biopsy 309


title: genomic DNA from skin peri-umbilical punch biopsy 293

source_name: skin peri-umbilical punch biopsy 293


title: genomic DNA from skin peri-umbilical punch biopsy 303

source_name: skin peri-umbilical punch biopsy 303


title: genomic DNA from skin peri-umbilical punch biopsy 299

source_name: skin peri-umbilical punch biopsy 299


title: genomic DNA from skin peri-umbilical punch biopsy 317

source_name: skin peri-umbilical punch biopsy 317


title: genomic DNA from skin peri-umbilical punch biopsy 295

source_name: skin peri-umbilical punch biopsy 295


title: genomic DNA from skin peri-umbilical punch biopsy 318

source_name: skin peri-umbilical punch biopsy 318


title: genomic DNA from skin peri-umbilical punch biopsy 307

source_name: skin peri-umbilical punch biopsy 307


title: genomic DNA from skin peri-umbilical punch biopsy 297

source_name: skin peri-umbilical punch biopsy 297


title: genomic DNA from skin peri-umbilical punch biopsy 298

source_name: skin peri-umbilical punch biopsy 298


title: genomic DNA from skin peri-umbilical punch biopsy 321

source_name: skin peri-umbilical punch biopsy 321


title: genomic DNA from skin peri-umbilical punch biopsy 314

source_name: skin peri-umbilical punch biopsy 314


title: genomic DNA from skin peri-umbilical punch biopsy 320

source_name: skin peri-umbilical punch biopsy 320


title: genomic DNA from skin peri-umbilical punch biopsy 292

source_name: skin peri-umbilical punch biopsy 292


title: genomic DNA from skin peri-umbilical punch biopsy 289

source_name: skin peri-umbilical punch biopsy 289


title: genomic DNA from skin peri-umbilical punch biopsy 287

source_name: skin peri-umbilical punch biopsy 287


title: genomic DNA from skin peri-umbilical punch biopsy 288

source_name: skin peri-umbilical punch biopsy 288


title: genomic DNA from skin peri-umbilical punch biopsy 291

source_name: skin peri-umbilical punch biopsy 291