title: 22_1220.1F.R135P, Experimental replicate 1

source_name: Soybean cultivar RIL 135 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 25_1234.1F.R143P, Experimental replicate 1

status: Public on May 30 2008

type: RNA

city: Blacksburg

first: sucheta

last: Tripathy

state: VA

address: 1, Washington street

department: Virginia  Bioinformatics Institute

country: USA

institute: Virginia Tech

description: Data was collected from the hypocotyl regions of Soybean plants at different time points

hyb_protocol: hybridization cocktail is prepared, including the fragmented target, probe array controls, BSA, and herring sperm DNA. It is then hybridized to the probe array during a 16-hour incubation(Affymetrix technical manual - 2004)

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

data_processing: The data were analyzed with RMA suite from R package version 2.4.0. Background correction was using RMA followed by quantile normalization and data was summarized using median polish method

label: biotin

molecule: total RNA

organism: Glycine max

source_name: Soybean cultivar RIL 143 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. RNA is is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets are then cleaned up, fragmented, and hybridized to GeneChip expression arrays(Affymetrix Technical manual - 2004)

growth_protocol: Soybean plants were grown in growth chambers and later transferred to trays with clothes soaked in water

extract_protocol: QIAGEN RNeasy Kit : As recommended by manufacturer

treatment_protocol: Soybean plants were grown in growth chambers and transferred to trays prior to inoculation. There were 3 trays for each treatment type having 10 plants each. P.sojae materials were inoculated onto the roots of the host plant and RNA extraction was carried out either on 3rd day or 5th day post inoculation. For mock inoculation, the plants were inoculated with pure water with agar. For RIL experiments the RILS had no specific time points but the checks did.

tag: cultivar - RIL 143

tag: Tissue/Cell Type

value: Soybean root/hypocotyls - P.sojae mycelium from minimal medium


title: 36_1223.1F.R137L, Experimental replicate 1

source_name: Soybean cultivar RIL 137 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 137


title: 2_C093.1F.R9F1U, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation

tag: cultivar - VP RIL 9 - susceptible line


title: 16_1216.1F.R132P, Experimental replicate 1

source_name: Soybean cultivar RIL 132 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 132


title: 4day_DMSO-treated_4h_rep2

status: Public on Jan 01 2009

city: Cambridge

first: Yuriy

middle: O.

last: Alekseyev

state: MA

address: 77 Massachusetts ave, bldg. 56-686

department: BE

description: 4-day-old mice were treated i.p. with a single dose (10 ml/kg) of DMSO and sacrificed 4h after treatment

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Log (base 2) transformed, RMA (quantile) normalized across 4-day-old AFB1-treated (n=3) and DMSO-treated (n=3) replicates (sacrificed 4 h after treatment)

organism: Mus musculus

source_name: 4-day-old, DMSO-treated, sacrificed 4 hours after treatment

label_protocol: Affymetrix

extract_protocol: Affymetrix

treatment_protocol: Single i.p. treatment with 10 ml/kg DMSO

tag: Strain

value: B6C3F1, Gender:male, Tissue:liver, Age:4 days


title: 24_C103.1F.R9F3L, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 38_C105.1F.SLF3L, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation

tag: cultivar - SLOAN - susceptible line


title: 11_1217.1F.R133U, Experimental replicate 1

source_name: Soybean cultivar RIL 133 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 133


title: 12_C107.1F.V7F3U, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation

tag: cultivar - V71-370 - resistant line


title: 20_C096.1F.SLF1P, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation


title: 86_C079.1E.R9E2U, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 10_C091.1F.V7F1L, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 8_C089.1E.R9E3U, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 1_1231.1F.R142L, Experimental replicate 1

source_name: Soybean cultivar RIL 142 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 142


title: 27_C101.1F.R9F2U, Experimental replicate 1


title: 23_C092.1F.V7F1P, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation


title: 9_1164.1E.R102P, Experimental replicate 1

source_name: Soybean cultivar RIL 102 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 102


title: 19_1227.1F.R139L, Experimental replicate 1

source_name: Soybean cultivar RIL 139 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 139


title: 15_1210.1F.R129P, Experimental replicate 1

source_name: Soybean cultivar RIL 129 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 129


title: 13_1229.1F.R141U, Experimental replicate 1

source_name: Soybean cultivar RIL 141 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 141


title: 17_1209.1F.R129U, Experimental replicate 1

source_name: Soybean cultivar RIL 129 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 82_1181.1E.R111L, Experimental replicate 1

source_name: Soybean cultivar RIL 111 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 111


title: 78_1173.1E.R107U, Experimental replicate 1

source_name: Soybean cultivar RIL 107 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 107


title: 77_C077.1E.SLE1L, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 74_1189.1E.R115L, Experimental replicate 1

source_name: Soybean cultivar RIL 115 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 115


title: 81_1193.1E.R117U, Experimental replicate 1

source_name: Soybean cultivar RIL 117 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 117


title: 84_1165.1E.R103U, Experimental replicate 1

source_name: Soybean cultivar RIL 103 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 103

tag: Tissue/Cell Type


title: 85_1171.1E.R106U, Experimental replicate 1

source_name: Soybean cultivar RIL 106 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 106


title: 7_C085.1E.SLE3U, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 83_1183.1E.R112U, Experimental replicate 1

source_name: Soybean cultivar RIL 112 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 112


title: 71_1183.1E.R112L, Experimental replicate 1

source_name: Soybean cultivar RIL 112 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 79_1196.1E.R119P, Experimental replicate 1

source_name: Soybean cultivar RIL 119 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 119


title: 76_1191.1E.R116L, Experimental replicate 1

source_name: Soybean cultivar RIL 116 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 116


title: 75_C081.1E.SLE2U, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation

tag: cultivar - SLOAN - susceptible line


title: 70_C087.1E.V7E3U, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation

tag: cultivar - V71-370 - resistant line


title: 72_1188.1E.R114P, Experimental replicate 1

source_name: Soybean cultivar RIL 114 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 114


title: 73_1169.1E.R105U, Experimental replicate 1

source_name: Soybean cultivar RIL 105 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 105


title: 6_1174.1E.R107P, Experimental replicate 1

source_name: Soybean cultivar RIL 107 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 68_1189.1E.R115U, Experimental replicate 1

source_name: Soybean cultivar RIL 115 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: Adult_DMSO-treated_4h_5ml/kg_rep1

description: Adult mice were treated i.p. with a single dose of DMSO (5 ml/kg) and sacrificed 4h after treatment

data_processing: Log (base 2) transformed, RMA normalized across adult DMSO-treated (n=3) and AFB1-treated (n=3) replicates (5 ml/kg, sacrificed 4 h after treatment)

source_name: Adult, DMSO-treated (5 ml/kg), sacrificed 4 hours after treatment

extract_protocol: Qiagen RNeasy

treatment_protocol: Single i.p. treatment with 5 ml/kg of DMSO

tag: Strain

value: B6C3F1, Gender:male, Tissue:liver, Age:adult (60-80 days)


title: 65_C084.1E.V7E2P, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 2 days post inoculation


title: 80_1172.1E.R106P, Experimental replicate 1

source_name: Soybean cultivar RIL 106 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 69_1186.1E.R113P, Experimental replicate 1

source_name: Soybean cultivar RIL 113 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 113


title: 67_1200.1E.R123P, Experimental replicate 1

source_name: Soybean cultivar RIL 123 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 123


title: 64_1199.1E.R123U, Experimental replicate 1

source_name: Soybean cultivar RIL 123 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 63_C080.1E.R9E2P, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 2 days post inoculation

tag: cultivar - VP RIL 9 - susceptible line


title: 66_1177.1E.R109L, Experimental replicate 1

source_name: Soybean cultivar RIL 109 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 109


title: 60_1170.1E.R105P, Experimental replicate 1

source_name: Soybean cultivar RIL 105 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 62_C083.1E.V7E2L, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 59_1194.1E.R117P, Experimental replicate 1

source_name: Soybean cultivar RIL 117 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 54_C083.1E.V7E2U, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 46_1167.1E.R104L, Experimental replicate 1

source_name: Soybean cultivar RIL 104 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 104


title: 47_C077.1E.SLE1U, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 51_1178.1E.R109P, Experimental replicate 1

source_name: Soybean cultivar RIL 109 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 52_1166.1E.R103P, Experimental replicate 1

source_name: Soybean cultivar RIL 103 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 43-1169.1E.R105L, Experimental replicate 1

source_name: Soybean cultivar RIL 105 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 41_C088.1E.V7E3P, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 3 days post inoculation


title: 4_1190.1E.R115P, Experimental replicate 1

source_name: Soybean cultivar RIL 115 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 115


title: 53_1191.1E.R116U, Experimental replicate 1

source_name: Soybean cultivar RIL 116 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 57_C086.1E.SLE3P, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 3 days post inoculation


title: 44_1182.1E.R111P, Experimental replicate 1

source_name: Soybean cultivar RIL 111 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 111


title: 3_1185.1E.R113U, Experimental replicate 1

source_name: Soybean cultivar RIL 113 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: Tissue/Cell Type


title: 58_C085.1E.SLE3L, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 37_1195.1E.R119L, Experimental replicate 1

source_name: Soybean cultivar RIL 119 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 32_1187.1E.R114U, Experimental replicate 1

source_name: Soybean cultivar RIL 114 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 31_1193.1E.R117L, Experimental replicate 1

source_name: Soybean cultivar RIL 117 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 117


title: 34_1171.1E.R106L, Experimental replicate 1

source_name: Soybean cultivar RIL 106 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 106


title: 49_C073.1E.V7E1L, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 5_1163.1E.R102U, Experimental replicate 1

source_name: Soybean cultivar RIL 102 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 102


title: 35_1175.1E.R108L, Experimental replicate 1

source_name: Soybean cultivar RIL 108 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 108


title: 38_C087.1E.V7E3L, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 40_1184.1E.R112P, Experimental replicate 1

source_name: Soybean cultivar RIL 112 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 112


title: 42_C076.1E.R9E1P, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation


title: 36_C081.1E.SLE2L, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation

tag: cultivar - SLOAN - susceptible line


title: 33_C074.1E.V7E1P, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation

tag: cultivar - V71-370 - resistant line


title: 39_C075.1E.R9E1L, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 28_1185.1E.R113L, Experimental replicate 1

source_name: Soybean cultivar RIL 113 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 23_C078.1E.SLE1P, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation


title: 25_1199.1E.R123L, Experimental replicate 1

source_name: Soybean cultivar RIL 123 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 1_1165.1E.R103L, Experimental replicate 1

source_name: Soybean cultivar RIL 103 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 103


title: 48_1168.1E.R104P, Experimental replicate 1

source_name: Soybean cultivar RIL 104 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 56_C075.1E.R9E1U, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 29_1167.1E.R104U, Experimental replicate 1

source_name: Soybean cultivar RIL 104 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 20_C079.1E.R9E2L, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 19_C089.1E.R9E3L, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 16_1192.1E.R116P, Experimental replicate 1

source_name: Soybean cultivar RIL 116 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 116


title: 21_1163.1E.R102L, Experimental replicate 1

source_name: Soybean cultivar RIL 102 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 18_1177.1E.R109U, Experimental replicate 1

source_name: Soybean cultivar RIL 109 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 14_1175.1E.R108U, Experimental replicate 1

source_name: Soybean cultivar RIL 108 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 22_C090.1E.R9E3P, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 3 days post inoculation


title: 30_1187.1E.R114L, Experimental replicate 1

source_name: Soybean cultivar RIL 114 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 114


title: 11_1173.1E.R107L, Experimental replicate 1

source_name: Soybean cultivar RIL 107 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 107


title: 10_1195.1E.R119U, Experimental replicate 1

source_name: Soybean cultivar RIL 119 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 119


title: 13_1181.1E.R111U, Experimental replicate 1

source_name: Soybean cultivar RIL 111 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 17_C082.1E.SLE2P, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 2 days post inoculation


title: 15_C073.1E.V7E1U, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 81_1053.1B.R031L, Experimental replicate 1

source_name: Soybean cultivar RIL 031 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 031


title: 87_1049.1B.R028U, Experimental replicate 1

source_name: Soybean cultivar RIL 028 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 028


title: 78_C034.1B.R9B3P, Experimental replicate 1

tag: cultivar - VP RIL 9 - susceptible line


title: 80_C027.1B.V7B2L, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 7_1054.1B.R031P_new, Experimental replicate 1

source_name: Soybean cultivar RIL 031 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 12_1176.1E.R108P, Experimental replicate 1

source_name: Soybean cultivar RIL 108 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 85_1049.1B.R028L, Experimental replicate 1

source_name: Soybean cultivar RIL 028 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 79_1046.1B.R025P, Experimental replicate 1

source_name: Soybean cultivar RIL 025 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 025


title: 70_1044.1B.R024P, Experimental replicate 1

source_name: Soybean cultivar RIL 024 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 024

tag: Tissue/Cell Type


title: 64_C020.1B.R9B1P, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation


title: 69_C021.1B.SLB1L, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 68_C019.1B.R9B1L, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 63_1047.1B.R027U, Experimental replicate 1

source_name: Soybean cultivar RIL 027 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 027


title: 62_C024.1B.V7B1P, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation


title: 67_1050.1B.R028P, Experimental replicate 1

source_name: Soybean cultivar RIL 028 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 61_C019.1B.R9B1U, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 60_1047.1B.R027L, Experimental replicate 1

source_name: Soybean cultivar RIL 027 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 72_C036.1B.SLB3P, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 3 days post inoculation


title: 5_C027.1B.V7B2U, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 52_C031.1B.V7B3U, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 49_C033.1B.R9B3L, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 6_C033.1B.R9B3U, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 76_C032.1B.V7B3P, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 3 days post inoculation


title: 44_C023.1B.V7B1L, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 37_1051.1B.R029U, Experimental replicate 1

source_name: Soybean cultivar RIL 029 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 029


title: 56_C025.1B.SLB2U, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 58_1043.1B.R024L, Experimental replicate 1

source_name: Soybean cultivar RIL 024 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 45_1051.1B.R029L, Experimental replicate 1

source_name: Soybean cultivar RIL 029 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 35_C030.1B.R9B2P, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 2 days post inoculation


title: 31_1045.1B.R025U, Experimental replicate 1

source_name: Soybean cultivar RIL 025 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 4_1048.1B.R027P, Experimental replicate 1

source_name: Soybean cultivar RIL 027 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 40_C023.1B.V7B1U, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 28_1045.1B.R025L, Experimental replicate 1

source_name: Soybean cultivar RIL 025 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 47_C021.1B.SLB1U, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 29_C035.1B.SLB3U, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 25_C029.1B.R9B2L, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 3_1053.1B.R031U, Experimental replicate 1

source_name: Soybean cultivar RIL 031 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 23_1052.1B.R029P, Experimental replicate 1

source_name: Soybean cultivar RIL 029 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 18_C022.1B.SLB1P, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation


title: 78-1004.1A.R002P, Experimental replicate 1

source_name: Soybean cultivar RIL 002 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 002


title: 1_C035.1B.SLB3L, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 86-C016.1A.V7A3P, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 3 days post inoculation


title: 17_C025.1B.SLB2L, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 16_C029.1B.R9B2U, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 15_C026.1B.SLB2P, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 2 days post inoculation


title: 14_C031.1B.V7B3L, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 76_1023.1A.R013U, Experimental replicate 1

source_name: Soybean cultivar RIL 013 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 013


title: 75-1013.1A.R008U, Experimental replicate 1

source_name: Soybean cultivar RIL 008 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 008


title: 8-1023.1A.R013L, Experimental replicate 1

source_name: Soybean cultivar RIL 013 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 9-1003.1A.R002L, Experimental replicate 1

source_name: Soybean cultivar RIL 002 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 69-1017.1A.R010U, Experimental replicate 1

source_name: Soybean cultivar RIL 010 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 010


title: 7-1011.1A.R007U, Experimental replicate 1

source_name: Soybean cultivar RIL 007 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 007


title: 19_C028.1B.V7B2P, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 2 days post inoculation

tag: cultivar - V71-370 - resistant line


title: 79-C011.1A.SLA2U, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation

tag: cultivar - SLOAN - susceptible line


title: 72-C002.1A.V7A1P, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation


title: 81-C005.1A.SLA1U, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 22_1043.1B.R024U, Experimental replicate 1

source_name: Soybean cultivar RIL 024 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 74-C018.1A.R9A3P, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 3 days post inoculation


title: 66-1009.1A.R006U, Experimental replicate 1

source_name: Soybean cultivar RIL 006 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 006


title: 70_C004.1A.R9A1P, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation


title: 71_1021.1A.R012U, Experimental replicate 1

source_name: Soybean cultivar RIL 012 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 012


title: 65-1001.1A.R001U, Experimental replicate 1

source_name: Soybean cultivar RIL 001 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 001


title: 64_1007.1A.R004U, Experimental replicate 1

source_name: Soybean cultivar RIL 004 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 004


title: 67-C015.1A.V7A3U, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 63-C001.1A.V7A1U, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 5_C008.1A.V7A2P, Experimental replicate 1


title: 62-1021.1A.R012L, Experimental replicate 1

source_name: Soybean cultivar RIL 012 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 61-1003.1A.R002U, Experimental replicate 1

source_name: Soybean cultivar RIL 002 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 59_C014.1A.SLA3P, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 3 days post inoculation


title: 47-1025.1A.R014U, Experimental replicate 1

source_name: Soybean cultivar RIL 014 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 014


title: Glucose- Glycerol late log phase 2

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

description: Slides were scanned Using Perkin Elmer Scanarray.

hyb_protocol: Hybridization performed exactly as described in Marr et al., J Bacteriol. 2006 Jun;188(11):3887-901

scan_protocol: scanning software: ScanArray express software version: 3.0

data_processing: VALUE: log2 transformed ratio of normalized medians normalization method: LOWESS algorithm

label: Cyanine 5

organism: Listeria monocytogenes

source_name: Wild type Listeria monocytogenes EGDe

label_protocol: Labeling performed exactly as described in Marr et al., J Bacteriol. 2006 Jun;188(11):3887-901

extract_protocol: RNA was isolated using RNeasy kit from Qiagen according to the manufacturers protocol with modifications as indicated in Marr et al., J Bacteriol. 2006 Jun;188(11):3887-901.

tag: Wild type Listeria monocytogenes EGDe grown in minimal medium with glucose to OD 600 nm 1.0 - late log phase and cells were harvested.

label: Cyanine 3

tag: Wild type Listeria monocytogenes EGDe grown in minimal medium with glycerol to OD 600 nm 1.0 - late log phase and cells were harvested.


title: 48_1017.1A.R010L, Experimental replicate 1

source_name: Soybean cultivar RIL 010 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: Tissue/Cell Type


title: 50-C013.1A.SLA3L, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 45_C015.1A.V7A3L, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 58_C009.1A.R9A2U, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation

tag: cultivar - VP RIL 9 - susceptible line


title: 57_1024.1A.R013P, Experimental replicate 1

source_name: Soybean cultivar RIL 013 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 53-1026.1A.R014P, Experimental replicate 1

source_name: Soybean cultivar RIL 014 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 4_C007.1A.V7A2L, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: Cellobiose-Glycerol late log phase 1

tag: Wild type Listeria monocytogenes EGDe grown in minimal medium with cellobiose to OD 600 nm 1.0 - late log phase and cells were harvested.


title: Cellobiose-Glycerol early log phase 2

tag: Wild type Listeria monocytogenes EGDe grown in minimal medium with cellobiose to OD 600 nm 0.5 - early log phase and cells were harvested.

tag: Wild type Listeria monocytogenes EGDe grown in minimal medium with glycerol to OD 600 nm 0.5 - early log phase and cells were harvested.


title: 55-1011.1A.R007L, Experimental replicate 1

source_name: Soybean cultivar RIL 007 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 56_1012.1A.R007P, Experimental replicate 1

source_name: Soybean cultivar RIL 007 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 43-C017.1A.R9A3U, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation


title: 51-C003.1A.R9A1L, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: Glucose-Glycerol early log phase 2

tag: Wild type Listeria monocytogenes EGDe grown in minimal medium with glucose to OD 600 nm 0.5 - early log phase and cells were harvested.


title: 42_1001.1A.R001L, Experimental replicate 1

source_name: Soybean cultivar RIL 001 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 41-C011.1A.SLA2L, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: 49-1019.1A.R011U, Experimental replicate 1

source_name: Soybean cultivar RIL 011 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 011


title: Glucose-Glycerol early log phase 1


title: Cellobiose-Glycerol early log phase 1


title: 46_1005.1A.R003L, Experimental replicate 1

source_name: Soybean cultivar RIL 003 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 003


title: Cellobiose-Glycerol late log phase 2


title: 34-1006.1A.R003P, Experimental replicate 1

source_name: Soybean cultivar RIL 003 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 38-C005.1A.SLA1L, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: Glucose-Cellobiose Early log phase 2

data_processing: VALUE: log2 transformed ratio of normalized medians (Cellobiose/Glucose); normalization method: LOWESS algorithm

source_name: Wild type Listeria monocytogenes EGDe


title: Glucose-Cellobiose late log phase 1


title: 31-1007.1A.R004L, Experimental replicate 1

source_name: Soybean cultivar RIL 004 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 29-C006.1A.SLA1P, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 1 days post inoculation


title: 30-C012.1A.SLA2P, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 2 days post inoculation


title: 3-1005.1A.R003U, Experimental replicate 1

source_name: Soybean cultivar RIL 003 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: 33_1020.1A.R011P, Experimental replicate 1

source_name: Soybean cultivar RIL 011 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: Glucose-Cellobiose Early log phase 1

data_processing: VALUE: log2 transformed ratio of normalized medians; normalization method: LOWESS algorithm


title: 36_1014.1A.R008P, Experimental replicate 1

source_name: Soybean cultivar RIL 008 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 008


title: Cellobiose-Glycerol late log phase 3


title: 28_1025.1A.R014L, Experimental replicate 1

source_name: Soybean cultivar RIL 014 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: Cellobiose-Gylcerol early log phase 3


title: Cellobiose-Gylcerol late log phase 4


title: 26-C003.1A.R9A1U, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 days post inoculation


title: 27-C007.1A.V7A2U, Experimental replicate 1

source_name: Soybean cultivar V71-370 - resistant line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation

tag: cultivar - V71-370 - resistant line


title: Cellobiose-Glycerol early log phase 4


title: Glucose-Glycerol late log phase 1

tag: Wild type Listeria monocytogenes EGDe grown in minimal medium with glycerolto OD 600 nm 1.0 - late log phase and cells were harvested.


title: Glucose-Glycerol late log phase 4


title: 24_1018.1A.R010P, Experimental replicate 1

source_name: Soybean cultivar RIL 010 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 010


title: 23_1022.1A.R012P, Experimental replicate 1

source_name: Soybean cultivar RIL 012 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 012


title: Glucose-Cellobiose late log phase 3


title: 2-1008.1A.R004P, Experimental replicate 1

source_name: Soybean cultivar RIL 004 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 004


title: 21-1019.1A.R011L, Experimental replicate 1

source_name: Soybean cultivar RIL 011 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: Glucose-Glycerol early log phase 4


title: Glucose-Glycerol late log phase 3


title: Glucose-Glycerol early log phase 3


title: 20-C013.1A.SLA3U, Experimental replicate 1

source_name: Soybean cultivar SLOAN - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation

tag: cultivar - SLOAN - susceptible line


title: 19_C009.1A.R9A2L, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 2 days post inoculation


title: Glucose-Cellobiose late log phase 2

tag: Wild type Listeria monocytogenes EGDe grown in minimal medium with glucose to OD 600 nm 1.0 - late log phase and cells were harvested.


title: Glucose-Cellobiose early log phase 4


title: 18-1009.1A.R006L, Experimental replicate 1

source_name: Soybean cultivar RIL 006 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 006


title: 14-C017.1A.R9A3L, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation

tag: Tissue/Cell Type


title: Glucose-Cellobiose Early log phase 3

source_name: Wild type Listeria monocytogenes EGDe


title: 15-1002.1A.R001P, Experimental replicate 1

source_name: Soybean cultivar RIL 001 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA

tag: cultivar - RIL 001


title: Hypothalamus-Mecp2-null C57BL/6J-biological rep4

city: Houston

first: Maria

last: Chahrour

state: TX

address: 1 Baylor Plaza, T836

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Gene expression data

hyb_protocol: Following fragmentation of 15.0 mg of the labeled cRNA, a hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip array.  The array was hybridized 16 hours

scan_protocol: The array was stained using the EukGEws2v5 protocol on the Fluidics Station 450.  The stained array was scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The images were analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.1 and scale factor of 500. Subsequently, R based analysis using exonmap package and rma normalization

source_name: Hypothalamus, Mecp2-null

label_protocol: Total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the in vitro transcription reaction, producing biotin-labeled

extract_protocol: Total RNA was extracted from the hypothalamus of 6 weeks old male mice using TRIzol reagent, DNaseI treated, and purified using the RNeasy mini kit, all according to the manufacturers protocols

tag: genotype

tag: gender

value: male

tag: age

value: 6 weeks

tag: strain


title: Hypothalamus-wild type C57BL/6J-biological rep2

description: Gene expression data

source_name: Hypothalamus, wild type

value: wild type


title: 12-1010.1A.R006P, Experimental replicate 1

source_name: Soybean cultivar RIL 006 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA


title: 13-1013.1A.R008L, Experimental replicate 1

source_name: Soybean cultivar RIL 008 - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA


title: Hypothalamus-Mecp2-null C57BL/6J-biological rep3

description: Gene expression data


title: Hypothalamus-wild type C57BL/6J-biological rep4

description: Gene expression data


title: Hypothalamus-wild type C57BL/6J-biological rep3

description: Gene expression data


title: Human blood treated with LPS (control pool) vs. LPS (individual #4)

status: Public on May 29 2008

city: Kirkland

first: Alex

middle: G.

last: Therien

address: 17611 Transcanada Hwy.

department: Biochemistry and Molecular Biology

country: Canada

institute: Merck Frosst Canada, Ltd.

description: Mutual Antagonistic Relationship Between Prostaglandin E2 and Interferon-(gamma): Implications for Rheumatoid Arthritis. Marie-Claude Mathieu, Simon Lord-Dufour, Virginie Bernier, Yves Boie, Jason D. Burch, Patsy Clark, Danielle Denis, Yongxin Han, James R. Mortimer and Alex G. Therien. Eur. J. Immunol 2008.  The samples consisted of leukocytes isolated from human blood following treatment with LPS (1 ug/ml), with or without L-902688 (100 nM), and  with or without MF498 (1 uM). They were compared as specified in the data set titles, to measure the effects of EP4 agonism or EP4 antagonism on global gene expression.  The data reported here are the microarray data as processed by the standard Rosetta Resolver(R) ratio method.  The data were additionally processed according to the "Materials and Methods" section in order to arrive at the observations discussed in the paper.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

organism: Homo sapiens

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

source_name: Human blood treated with LPS (individual #4)

tag: LPS (individual #4)


title: UNKNOWN247

city: Boston

first: Roman

last: Yelensky

address: Massachusetts General Hospital Department of Molecular Biology 185 Cambridge St., Simches Ctr., CPZN-6818

institute: MGH

hyb_protocol: RNA was processed and hybridized onto Affymetrix Human U133A whole genome RNA expression genechip arrays according to the manufacturer’s protocol.

scan_protocol: As per manufacturer's protocol

data_processing: RMA; Gene expression summary values for the whole dataset were computed by RMA[36,37] and log-transformed. Measurements were successfully obtained for 257 HapMap cell lines in the main experiment, for 64 biological replicates, for 24 cell lines originally thawed at the WTSI, as well as multiple replicates of 5 cell lines derived from chimpanzees. (raw data in “all broad cell line expression data.zip” online)

source_name: Lymphoblastoid cell line

label_protocol: As per manufactureer's protocol. 1.25 ug total RNA (OD>1.8) was diluted to a total volume of 10uL.

growth_protocol: EBV-transformed lymphoblastoid cell lines were acquired from the NHGRI Sample Repository for Human Genetic Research in frozen aliquots.  Cells were thawed in 5mL culture medium (RPMI medium 1640 (Invitrogen) supplemented with 10% FetalPlex (Gemini), 2mM L-Glutamine (Invitrogen), and 1x penicillin/streptomycin (Invitrogen)).  Cell lines were counted daily using Z2 Coulter Counter (Beckman Coulter) and passaged as needed to maintain a concentration of 2-5 x 1e5 cells/ml at 37C in a 95% humidified 5% CO2 atmosphere.      Initially, cells were grown until 5 x 1e5 cells/ml were reached in 50 mL total volume.  Then, ten identical aliquots were frozen in 1 mL freezing media containing 50% FetalPlex, 40% RPMI 1640 medium, and 10% DMSO (Sigma) at -80C for 24 hrs and transferred to liquid nitrogen.  These aliquots were used to provide biologic replicates for the experiments described below.    Aliquots were thawed on experiment day #1 as described above.  Cell lines were counted daily and passaged as need to maintain a concentration of 4-8 x 1e5 cells/ml in 10 mL culture medium.  On experiment day #7, cells were counted and distributed for use in the various experiments described below.  One cc of culture was used for immediate immunophenotyping  via FACS and Luminex beads.  One cc of culture was used for RNA and DNA extraction using Trizol (Invitrogen) following the manufacturer's protocol.  The remaining eight cc of culture were used for drug response assays described below.

extract_protocol: All LCLs were cultured in the fashion described above.  Prior to the plating of cells for the Drug Response Assay, 5 x 10^5 cells were set aside for RNA extraction.  Cells were immediately lysed with Trizol Reagent (Invitrogen).  RNA was collected according to the manufacturer instructions.

tag: SAHA drug response

tag: Simva drug response

tag: 6MP drug response

tag: 5FU drug response

tag: MTX drug response


title: S006006_3

organism: Pan troglodytes


title: Hypothalamus-Mecp2-null C57BL/6J-biological rep2

description: Gene expression data


title: Human blood treated with LPS (control pool) vs. LPS and L-902688 (individual #2)

source_name: Human blood treated with LPS and L-902688 (individual #2)

tag: LPS and L-902688 (individual #2)


title: 10_C010.1A.R9A2P, Experimental replicate 1

source_name: Soybean cultivar VP RIL 9 - susceptible line - RNA taken from entire inoculated area inoculated with water + agar(mock sample): 2 days post inoculation

tag: cultivar - VP RIL 9 - susceptible line


title: Human blood treated with LPS (control pool) vs. LPS (individual #3)

source_name: Human blood treated with LPS (individual #3)

tag: LPS (individual #3)


title: Human blood treated with LPS (control pool) vs. LPS (individual #2)

source_name: Human blood treated with LPS (individual #2)

tag: LPS (individual #2)


title: Human blood treated with LPS (control pool) vs. LPS and L-902688 (individual #1)

source_name: Human blood treated with LPS and L-902688 (individual #1)

tag: LPS and L-902688 (individual #1)


title: Human blood treated with LPS (control pool) vs. LPS and L-902688 (individual #3)

source_name: Human blood treated with LPS and L-902688 (individual #3)

tag: LPS and L-902688 (individual #3)


title: Human blood treated with LPS and L-902688 (control pool) vs. LPS, L-902688 and MF498 (individual #3)

source_name: Human blood treated with LPS, L-902688 and MF498 (individual #3)

tag: LPS, L-902688 and MF498 (individual #3)


title: Human blood treated with LPS and L-902688 (control pool) vs. LPS, L-902688 and MF498 (individual #4)

source_name: Human blood treated with LPS, L-902688 and MF498 (individual #4)

tag: LPS, L-902688 and MF498 (individual #4)


title: Human blood treated with LPS (control pool) vs. LPS (individual #1)

source_name: Human blood treated with LPS (individual #1)

tag: LPS (individual #1)


title: S006006_2


title: Human blood treated with LPS and L-902688 (control pool) vs. LPS, L-902688 and MF498 (individual #1)

source_name: Human blood treated with LPS, L-902688 and MF498 (individual #1)

tag: LPS, L-902688 and MF498 (individual #1)


title: Human blood treated with LPS and L-902688 (control pool) vs. LPS, L-902688 and MF498 (individual #2)

source_name: Human blood treated with LPS, L-902688 and MF498 (individual #2)

tag: LPS, L-902688 and MF498 (individual #2)


title: Human blood treated with LPS (control pool) vs. LPS and L-902688 (individual #4)

source_name: Human blood treated with LPS and L-902688 (individual #4)

tag: LPS and L-902688 (individual #4)


title: Hypothalamus-MECP2-transgenic FVB-biological rep4

description: Gene expression data

source_name: Hypothalamus, MECP2-transgenic

tag: genotype

tag: gender

tag: age

tag: strain

value: FVB


title: Hypothalamus-Mecp2-null C57BL/6J-biological rep1

description: Gene expression data

source_name: Hypothalamus, Mecp2-null


title: S006006

tag: SAHA drug response

tag: Simva drug response

tag: 6MP drug response

tag: 5FU drug response

tag: MTX drug response


title: Hypothalamus-wild type C57BL/6J-biological rep1

description: Gene expression data

source_name: Hypothalamus, wild type


title: Hypothalamus-MECP2-transgenic FVB-biological rep3

description: Gene expression data


title: Hypothalamus-wild type FVB-biological rep4

description: Gene expression data


title: S003623_3


title: S003623_2


title: S003622_4


title: Hypothalamus-MECP2-transgenic FVB-biological rep1

description: Gene expression data


title: S003622_2


title: Hypothalamus-wild type FVB-biological rep3

description: Gene expression data


title: S003623_4


title: S003622


title: S003622_3


title: S003623


title: NA19240


title: S003612


title: S003610_2


title: Hypothalamus-wild type FVB-biological rep2

description: Gene expression data


title: Hypothalamus-MECP2-transgenic FVB-biological rep2

description: Gene expression data


title: S003610_3


title: S003610_4


title: S003612_2


title: Hypothalamus-wild type FVB-biological rep1

description: Gene expression data


title: S003612_4


title: NA19239


title: S003612_3


title: NA19238


title: S003610


title: NA19223


title: NA19222


title: NA19207_S


title: NA19205


title: NA19203


title: NA19210


title: NA19208


title: NA19209


title: NA19211


title: NA19207


title: NA19221


title: NA19202


title: NA19201


title: NA19204


title: NA19202_S


title: NA19194_2


title: NA19202_2


title: NA19200_2


title: NA19194_S


title: NA19200


title: NA19193


title: NA19194


title: NA19172_2


title: NA19171_S


title: NA19172


title: NA19192


title: NA19171


title: NA19171_2


title: NA19200_S


title: NA19172_S


title: NA19160


title: NA19159


title: NA19159_2


title: NA19154_S


title: NA19153


title: NA19152


title: NA19154_2


title: NA19145


title: NA19140


title: NA19144_S


title: NA19161


title: NA19141


title: NA19142


title: NA19144


title: NA19154


title: NA19138_S


title: NA19138


title: NA19139


title: NA19144_2


title: NA19138_2


title: NA19130


title: NA19137_S


title: NA19132


title: NA19137_2


title: NA19137


title: NA19131


title: NA19159_S


title: NA19119


title: NA19128


title: NA19103


title: NA19100


title: NA19098


title: NA19099


title: NA19116


title: NA19127


title: NA19102


title: NA19092


title: NA19094_S


title: NA19129


title: NA19094


title: NA19093


title: NA19003_2


title: NA19012


title: NA18997


title: NA19003


title: NA18998


title: NA19005


title: NA19120


title: NA19000


title: NA19101


title: NA19007


title: NA19094_2


title: NA18999


title: NA18995


title: NA18994


title: NA18978


title: NA18980


title: NA18992


title: NA18991


title: NA18975


title: NA18990


title: NA18981


title: NA18987


title: NA18976


title: NA18971


title: NA18973


title: NA18990_2


title: NA18972


title: NA18969


title: NA18967


title: NA18968


title: NA18966


title: NA18965


title: NA18959


title: NA18956


title: NA18964


title: NA18949


title: NA18974


title: NA18953


title: NA18949_2


title: NA18948_2


title: NA18952


title: NA18961


title: NA18960


title: NA18945


title: NA18945_2


title: NA18944


title: NA18914


title: NA18942_2


title: NA18942


title: NA18872_S


title: NA18872_2


title: NA18951


title: NA18912


title: NA18863_S


title: NA18947


title: NA18863_2


title: NA18943_2


title: NA18943


title: NA18940


title: NA18948


title: NA18870_2


title: NA18913


title: NA18872


title: NA18862_S


title: NA18870_S


title: NA18863


title: NA18871


title: NA18862_2


title: NA18862


title: NA18861


title: NA18854_2


title: NA18856_2


title: NA18860


title: NA18852_2


title: NA18854_S


title: NA18857


title: NA18855


title: NA18853


title: NA18636


title: NA18859


title: NA18856


title: NA18854


title: NA18852


title: NA18858


title: NA18635


title: NA18623_2


title: NA18637


title: NA18633_2


title: NA18623


title: NA18632


title: NA18622


title: NA18633


title: NA18852_S


title: NA18624


title: NA18856_S


title: NA18620_2


title: NA18620


title: NA18612


title: NA18608_2


title: NA18594


title: NA18582


title: NA18592


title: NA18611


title: NA18593


title: NA18608


title: NA18605


title: NA18621


title: NA18603


title: NA18593_2


title: NA18609


title: NA18576


title: NA18562


title: NA18573


title: NA18582_2


title: NA18563


title: NA18572_2


title: NA18570


title: NA18572


title: NA18564


title: NA18566


title: NA18558_2


title: NA18561


title: NA18571


title: NA18606


title: NA18552


title: NA18550


title: NA18542


title: NA18555_2


title: NA18540


title: NA18579


title: NA18552_2


title: NA18558


title: NA18545


title: NA18547


title: NA18529


title: NA18537


title: NA18524


title: NA18540_2


title: NA18526_2


title: NA18523


title: NA18523_2


title: NA18526


title: NA18555


title: NA18545_2


title: NA18523_S


title: NA18522


title: NA18516


title: NA18515_S


title: NA18521


title: NA18515_2


title: NA18515


title: NA18517


title: NA12892


title: NA18505


title: NA18507


title: NA18504_S


title: NA18504


title: NA18505_2


title: NA18505_S


title: NA12878


title: NA18504_2


title: NA18501_2


title: NA12872


title: NA18506


title: NA18501


title: NA12891


title: NA18502


title: NA12864


title: NA12875


title: NA18501_S


title: NA12873_2


title: NA12865


title: NA12814


title: NA18500


title: NA18503


title: NA12874


title: NA12815


title: NA12813


title: NA12873


title: NA12812


title: NA12802


title: NA12761


title: NA12264_2


title: NA12707


title: NA12763


title: NA12760


title: NA12753_2


title: NA12801_2


title: NA12762_2


title: NA12751_2


title: NA12762


title: NA12801


title: NA12750


title: NA12753


title: NA12752_2


title: NA12717


title: NA12264


title: NA12249


title: NA12751


title: NA12248


title: NA12239


title: NA12234


title: NA12156_2


title: NA12154


title: NA12154_2


title: NA12155


title: NA12146


title: NA12145_T1


title: NA12145_7


title: NA12249_2


title: NA12145_T2


title: NA12145_T3


title: NA12145_5


title: FW040023, BHIB/pH 5.0 + SD, biological replicate #2, technical replicate #2

city: Hobart

first: John

middle: Phillip

last: Bowman

state: Tasmania

address: College Road, Sandy Bay

department: School of Agricultural Science

country: Australia

institute: University of Tasmania

description: No additional information

hyb_protocol: Slides were pre-hybdridised in a hybrisation solution (25% vol./vol. formamide, 5 x SSC buffer â€“ 0.75 M NaCl, 0.075 M trisodium citrate, pH 7.0, 0.1% sodium dodecyl sulfate) containing 10 mg ml-1 bovine serum albumin for 45 min at 42Â°C. Slides were then rinsed twice in distilled water and air-dryed. Hybridisation was performed in a humid hybridisation chamber at 42Â°C for 16-20 h using a hybridisation solution containing 0.42 ug ul-1 human Cot1 DNA, 0.62 ug ul-1 polyA and 0.83 ug ul-1 salmon sperm DNA. Slides were washed at room temperature in 1x SSC buffer containing 0.2% SDS for 5 min and again in 0.1 ï‚´ SSC buffer containing 0.2% SDS for 5 min. The slides were then further washed twice in 0.1 x SSC buffer at room temperature for 2 min. Slides were then air dried.

scan_protocol: GenePix 4000B scanner (Axon Instruments) to create a TIFF file. TIFF files were then analysed in GenePix Pro 3.0 to generate a GPR file.

data_processing:
Normalization of raw data and subsequent statistical testing was performed with the WebArray Online platform (Xia et al., 2005). Within-array normalization used the global LOESS procedure. Between each array quantile normalization was used to ensure intensities had the same empirical distribution across arrays and across channels. The significance of differential expression was analysed using linear modal statistical analysis. Spacings LOESS histogram analysis (using WebArray) and the program EDGE (Leek et al., 2006) were used to estimate the conditional false discovery rate (FDR), the expected proportion of false positives conditioned on having k 'significant' findings (Pounds & Cheng, 2004).
Leek, J. T., Monsen, E., Dabney, A. R., and Storey, J. D. 2006. EDGE: extraction and analysis of differential gene expression. Bioinformatics 22:507-508.
Pounds, S., and Cheng, C. 2004. Improving false discovery rate estimation. Bioinformatics 20:1737-1745.
Xia, X. Q.; McClelland, M., and Wang, Y. P. 2005. WebArray: an online platform for microarray data analysis. BMC Informatics 6: article 306.

label_protocol: RNA was converted to cDNA and postlabelled with Cy5 (red) fluorescent dye using the SuperScript Indirect cDNA Labelling System (Invitrogen).

growth_protocol: Exponential phase culture, brain heart infusion broth at pH 5.0 containing 21 mM sodium diacetate. Inoculum was pre-habituated to growth at pH 5.0. Qiagen RNA Protect reagent used for RNA stabilization.

extract_protocol: Cell pellets were defrosted and underwent a 6 h (25Â°C) enzymatic treatment in TE buffer (10 mM Tris HCl, 1 mM disodium EDTA, pH 7.5) containing 20 mg ml-1 lysozyme and 10 mg ml-1 proteinase K. Cells were suspended in RNAeasy MIDI RNA extraction kit (Qiagen) lysis buffer containing 0.1% beta-mercaptoethanol and fully lysed by sonication. Sonication was performed using a Branson 450 sonifier using three 30 pulses at maximum power with samples placed on ice for 20 s between pulses. RNA was then extracted and purified using the RNAeasy kit and subsequently stored at -75Â°C. RNA quality and quantity was assessed with an Agilent Technologies bioanalyser 2100 and RNA LabChip.

tag: FW040023, lineage II, serotype 1/2c

label_protocol: RNA was converted to cDNA and postlabelled with Cy3 (green) fluorescent dye using the SuperScript Indirect cDNA Labelling System (Invitrogen).

growth_protocol: Exponential phase culture, habituated to brain heart infusion broth at pH 5.0. Qiagen RNA Protect reagent used for RNA stabilization.


title: NA12145


title: NA12144_2


title: NA12145_6


title: NA12752


title: FW040023, BHIB/pH 5.0 + SD vs pH 5.0, biological replicate #1, technical replicate #1

description: No additional information


title: FW040023, BHIB/pH 5.0 + SD vs pH 5.0, biological replicate #1, technical replicate #2

description: No additional information


title: FW040023, BHIB/pH 5.0 + SD vs pH 5.0, biological replicate #2, technical replicate #1

description: No additional information


title: NA12144


title: NA12145_4


title: NA12145_8


title: NA12145_3


title: NA12056


title: ATCC 19115, BHIB/pH 5.0 + SD vs pH 5.0, biological replicate #2, technical replicate #2

description: No additional information

source_name: ATCC 19115, BHIB/pH 5.0 + SD

tag: ATCC 19115, lineage I, serotype 4b

source_name: ATCC 19115, BHIB/pH 5.0


title: ATCC 19115, BHIB/pH 5.0 + SD, biological replicate #1, technical replicate #2

description: No additional information

source_name: ATCC 19115, BHIB/pH 5.0 +SD


title: ATCC 19115, BHIB/pH 5.0 + SD vs pH 5.0, biological replicate #2, technical replicate #1

description: No additional information


title: ATCC 19115, BHIB/pH 5.0 + SD vs. pH 5.0, biological replicate #1, technical replicate #1

description: No additional information


title: FW040023, BHIB/pH 5.0, biological replicate #2, technical replicate #2

description: No additional information

growth_protocol: Exponential phase culture, brain heart infusion broth at pH 7.2. Qiagen RNA Protect reagent used for RNA stabilization.


title: NA12057

source_name: Lymphoblastoid cell line


title: FW040023, BHIB/pH 5.0, biological replicate #1, technical replicate #2

description: No additional information


title: NA12043


title: NA12005_2


title: FW040023, BHIB/pH 5.0 vs pH 7.2, biological replicate #1, technical replicate #2

description: No additional information


title: NA12006


title: FW040023, BHIB/pH 5.0 vs pH 7,2, biological replicate #1, technical replicate #1

description: No additional information


title: ATCC 19115, BHIB/pH5.0 vs pH7.2, biological replicate #2, technical replicate #1

description: No additional information

hyb_protocol: Slides were pre-hybdridised in a hybrisation solution (25% vol./vol. formamide, 5 x SSC buffer [0.75 M NaCl, 0.075 M trisodium citrate], pH 7.0, 0.1% sodium dodecyl sulfate) containing 10 mg ml-1 bovine serum albumin for 45 min at 42Â°C. Slides were then rinsed twice in distilled water and air-dryed. Hybridisation was performed in a humid hybridisation chamber at 42°C for 16-20 h using a hybridisation solution containing 0.42 ug ul-1 human Cot1 DNA, 0.62 ug ul-1 polyA and 0.83 ug ul-1 salmon sperm DNA. Slides were washed at room temperature in 1x SSC buffer containing 0.2% SDS for 5 min and again in 0.1 ï‚´ SSC buffer containing 0.2% SDS for 5 min. The slides were then further washed twice in 0.1 x SSC buffer at room temperature for 2 min. Slides were then air dried.

extract_protocol: Cell pellets were defrosted and underwent a 6 h (25°C) enzymatic treatment in TE buffer (10 mM Tris HCl, 1 mM disodium EDTA, pH 7.5) containing 20 mg ml-1 lysozyme and 10 mg ml-1 proteinase K. Cells were suspended in RNAeasy MIDI RNA extraction kit (Qiagen) lysis buffer containing 0.1% beta-mercaptoethanol and fully lysed by sonication. Sonication was performed using a Branson 450 sonifier using three 30 pulses at maximum power with samples placed on ice for 20 s between pulses. RNA was then extracted and purified using the RNAeasy kit and subsequently stored at -75°C. RNA quality and quantity was assessed with an Agilent Technologies bioanalyser 2100 and RNA LabChip.


title: ATCC 19115, BHIB/pH 5.0 vs pH 7.2, biological replicate #1, technical replicate #1

description: No additional information

source_name: ATCC 19115, BHIB/pH 7.2


title: ATCC 19115, BHIB/pH 5.0 vs pH 7,2, biological replicate #2, technical replicate #2

description: No additional information


title: ATCC 19115, BHIB/pH 5.0 vs pH 7.2, biological replicate #1, technical replicate #2

description: No additional information

tag: ATCC 19115, lineage, serotype 4b


title: NA12044


title: NA11995_2


title: NA12003


title: NA12005


title: NA11994


title: NA11994_2


title: NA11881


title: NA11995


title: NA12145_2


title: NA12004


title: NA11882


title: NA11992


title: NA11840_2


title: NA11829


title: NA10856


title: NA10863


title: NA10831


title: NA11839


title: NA10863_2


title: NA10857


title: NA10860


title: NA10855


title: NA11840


title: NA10861


title: NA10859


title: NA11832


title: NA10851_2


title: NA10846_2


title: NA10838


title: NA10846


title: NA11830


title: NA10835


title: NA10847


title: NA10851


title: NA10830


title: NA10854


title: NA11831


title: NA07357


title: NA07357_2


title: NA07348_2


title: NA10839


title: MTB-deltadosST compdosT-NO rep2

city: San Francisco

first: Michael

last: Shiloh

state: CA

institute: University of California at San Francisco

description: Biological replicate 2

hyb_protocol: Cy5 and Cy3 labelled probes were mixed and hybridized to oligonucleotide MTB arrays (Operon Biosystems) at 63 C for 18h.After hybridization, slides were washed in batch.

scan_protocol: Slides were scanned using an Axon 4000B scanner and GenePix software. Data was acquired using Spotreader 1.3.1.0 and Acuity 4.0 software

data_processing: Ratio-based normalization, flagged features using Spotreader default parameters

organism: Mycobacterium tuberculosis

source_name: MTB- NO treated 100 uM

label_protocol: 5 ug total RNA was reverse transcribed into cDNA using random hexamer primers in the presence of aa-dUTP. cDNA was labelled with Cy dyes (Amersham) and purified over Zymo DNA binding columns.

growth_protocol: M. tuberculosis growing in 7H9 with 0.2% Tween 80 in early log phase

extract_protocol: RNA was extracted from 50 ml of culture by beadbeating in Trizol and RNA purified with Qiagen Rneasy columns per manufacturers instructions.

treatment_protocol: M. tuberculosis treated with 20000 ppm CO gas in the headspace or 100 uM DETANO in the medium for 60 minutes

tag: M. tuberculosis H37Rv delta-dosST complemented with dosT strain

source_name: MTB -Untreated


title: MTB-deltadosST-NO rep2

description: Biological replicate 2

tag: M. tuberculosis H37Rv delta-dosST strain


title: MTB-deltadosT-NO rep2

description: Biological replicate 2

tag: M. tuberculosis H37Rv delta-dosT strain


title: MTB-deltadosST-CO rep2

description: Biological replicate 2

source_name: MTB- CO treated 20000 ppm


title: MTB-deltadosS-CO rep2

description: Biological replicate 2

tag: M. tuberculosis H37Rv delta-dosS strain


title: MTB-deltadosT-CO rep2

description: Biological replicate 2


title: MTB WT-NO rep2

description: Biological replicate 2

tag: M. tuberculosis H37Rv strain


title: MTB WT-CO rep2

description: Biological replicate 2


title: NA07019


title: MTB-deltadosST compdosT-CO rep2

description: Biological replicate 2


title: MTB-deltadosST compdosT-NO rep1

description: Biological replicate 1


title: MTB-deltadosS-NO rep2

description: Biological replicate 2


title: NA07055


title: NA07022


title: NA07000


title: NA07348


title: NA07048


title: NA07034


title: MTB-deltadosT compdosT-NO rep1

description: Biological replicate 1

tag: M. tuberculosis H37Rv delta-dosT complemented with dosT strain


title: NA07345


title: NA07029


title: NA07056


title: NA06991


title: NA06993


title: MTB-deltadosST-NO rep1

description: Biological replicate 1


title: MTB-deltadosT-NO rep1

description: Biological replicate 1


title: NA06994


title: MTB WT-NO rep1

description: Biological replicate 1


title: MTB-deltadosS compdosS-NO rep1

description: Biological replicate 1

tag: M. tuberculosis H37Rv delta-dosS complemented with dosS strain


title: MTB-deltadosST compdosT-CO rep1

description: Biological replicate 1


title: MTB-deltadosS-NO rep1

description: Biological replicate 1


title: MTB-deltadosST-CO rep1

description: Biological replicate 1


title: MTB-deltadosT compdosT-CO rep1

description: Biological replicate 1


title: MTB-deltadosR-NO rep2

description: Biological replicate 2

tag: M. tuberculosis H37Rv delta-dosR strain


title: MTB-WT-NO rep2

description: Biological replicate 2


title: MTB WT-CO rep1

description: Biological replicate 1


title: MTB-deltadosT-CO rep1

description: Biological replicate 1


title: MTB-deltadosS-CO rep1

description: Biological replicate 1


title: MTB-deltadosR-CO rep2

description: Biological replicate 2


title: MTB-WT-CO rep2

description: Biological replicate 2


title: MTB-deltadosS compdosS-CO rep1

description: Biological replicate 1


title: MTB-deltadosR-NO rep1

description: Biological replicate 1


title: MTB_CO 200 ppm_rep1

description: Biological replicate 1

source_name: MTB- CO treated 200 ppm

treatment_protocol: M. tuberculosis treated with 2000, 200, 20 or 0 ppm CO gas in the headspace for 48 hours.

tag: M. tuberculosis Erdman strain


title: MTB-deltadosR compdosR-NO rep1

description: Biological replicate 1

tag: M. tuberculosis H37Rv delta-dosR complemented with dosR strain


title: MTB-WT-CO rep1

description: Biological replicate 1


title: MTB-WT-NO rep1

description: Biological replicate 1


title: MTB_CO 200 ppm_rep2

description: Biological replicate 2


title: MTB_CO 2000 ppm_rep2

description: Biological replicate 2

source_name: MTB- CO treated 2000 ppm


title: MTB_CO 20 ppm_rep2

description: Biological replicate 2

source_name: MTB- CO treated 20 ppm


title: MTB_CO 2000 ppm_rep1

description: Biological replicate 1


title: MTB-deltadosR compdosR-CO rep1

description: Biological replicate 1


title: MTB-deltadosR-CO rep1

description: Biological replicate 1


title: ES vs EB: ES DAY 0 normalised_data

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

institute: Institute for Molecular Bioscience, Uni of Qld

description:
Illumina data was used for direct comparisons to data generated by transcriptome sequencing of the
same samples on the SOLiD platform.

hyb_protocol: According to protocol provided by Sentrix Mouse-6 Expression BeadChip (Illumina)

scan_protocol: Image scanning hardware and software, and processing procedures and parameters: Illumina BeadStation 500; Illumina BeadStudio V2 no normalisation

data_processing:
Raw was processed using BeadStudio, V2
This data was subsequently processed by RMA background subtraction and quantile normalised through
limma in R. Output of this file was flagged dependent on precision score:
	P = 1;
	M >= 0.99;
	A < 0.99;

source_name: Mouse ES cells

label_protocol: as per instructions for Illumina labelling technique

extract_protocol: as per Instructions for QIAGEN RNeAsy mini kit

tag: RNA was extracted from pooled ES cells at day 0


title: MTB_CO 20 ppm_rep1

description: Biological replicate 1


title: XLMR patient (2007062803b_bis)

status: Public on May 27 2008

type: genomic

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: X chromosome-specific Array-CGH of XLMR patient

hyb_protocol: For each hybridisation, 1 µg of the Cy5- and 2 µg of the Cy3- labeled probes, with a specific activity < 40 were mixed together with 50 ¼g Cot-1 DNA (Invitrogen, Carlsbad, CA). Probe preparation, pre-blocking and washing of the slides was performed as described previously (Van Buggenhout G, et al. 2004. J. Med. Genet. 41: 691-698).

scan_protocol: Arrays were scanned at 532 nm (Cy3) and 635 nm (Cy5) using the Genepix 4000B scanner (Axon Instruments, Aberdeen, UK) and the acquired images were analyzed using the Genepix Pro software (Axon Instruments).

data_processing: Spot intensities were corrected for local background and only those spots with Cy5 as well as Cy3 signal intensities at least 1.7-fold above the local background, were further analyzed. For each clone, a ratio of Cy5 to Cy3 fluorescent intensity was calculated. Normalization of the data was achieved by dividing the fluorescent intensity ratio of each spot by the mean of the ratios of all spots. Finally, the normalized ratio values of the duplicates were averaged and a log2 value was calculated.

molecule: genomic DNA

label_protocol: Genomic DNA was labeled with the Bioprime DNA Labeling System (Invitrogen, Carlsbad, CA) using Cy3- and Cy5-labelled dCTP's (Amersham Biosciences, Buckinghamshire, UK) as described by the manufacturer. The concentrations and labeling efficiencies were measured with the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Rockland, DE).

extract_protocol: Genomic DNA from patients as well as from healthy controls was isolated from peripheral blood using the Wizard Genomic DNA purification Kit (Promega, Madison, WI) and using manufacture's protocol.

tag: control

tag: XLMR patient 46,XY


title: ES vs EB: EB DAY 4 normalised_data

source_name: Mouse EB Cells

tag: RNA was extracted from pooled EB cells at day 4


title: 2091 mock ChIP vs. 4 hours serum stimulated 2091 Myc ChIP set 2

first: Jonghwan

last: Kim

address: 1 Blackfan circle Karp-7

institute: HMS/CHB

description:
2091 mock ChIP vs. 4 hours serum stimulated 2091 Myc ChIP
4 hours after serum addition, ChIP performed.

data_processing: Data processed by using The Longhorn Array Database (LAD)

source_name: 2091 mock ChIP

tag: 2091 mock ChIP

source_name: 4 hours serum stimulated 2091 Myc ChIP

tag: 4 hours serum stimulated 2091 Myc ChIP


title: XLMR patient (2007062807b)


title: Genotype: Steptoe - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Steptoe, 7 day old seedling (first leaf unfolded), rep 3

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: leaf (genotype: Steptoe)

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  Seedlings were grown in the greenhouse for 7 days.  No supplemental lighting was used.

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: cultivar Steptoe (Germplasm Name); PO:0009025 leaf, (Organism Part); GRO:0007060 (Development Stage); 7 days (Age); garden soil (Growth Media).


title: Genotype: Morex - rep2

description: Morex, 7 day old seedling (first leaf unfolded), rep 2

source_name: leaf (genotype: Morex)

tag: cultivar Morex (Germplasm Name); PO:0009025 leaf, (Organism Part); GRO:0007060 (Development Stage); 7 days (Age); garden soil (Growth Media).


title: Genotype: Morex - rep3

description: Morex, 7 day old seedling (first leaf unfolded), rep 3


title: Fat line chickens, biological rep4

city: Harbin

first: Hongbao

last: Wang

address: No. 59 Mucai Street, Xiangfang District

country: China

institute: Northeast Agricultural University

description: Gene expression data from chicken adipose tissue at 7-week of age

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

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

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

organism: Gallus gallus

source_name: fat line chicken adipose tissue at 7-week of age

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

growth_protocol: All birds were kept in similar environmental conditions and had access to feed and water ad libitum, and were fed with a commercial corn-soybean-based diet that met all NRC requirements (National Research Council, 1994). From hatching to 3 weeks the birds received a starter feed (3,100 kcal ME/kg and 210 g/kg CP), and from 4 weeks to slaughter they were fed a grower diet (3,000 kcal ME/kg and 190 g/kg CP).

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

treatment_protocol: Birds were slaughtered at 7 weeks and abdominal fat was isolated, immediately frozen in liquid nitrogen and stored at -80oC.

tag: Strain

value: Arbor Acres breed,Gender:male

tag: Age

value: 49 day after birth


title: Genotype: Morex - rep1

description: Morex, 7 day old seedling (first leaf unfolded), rep 1


title: Fat line chickens, biological rep2


title: Genotype: Steptoe - rep2

description: Steptoe, 7 day old seedling (first leaf unfolded), rep 2


title: 2091 mock ChIP vs quiescent 2091 Myc ChIP set 2

description:
2091 mock ChIP vs quiescent 2091 Myc ChIP
Serum depletion for 72 hours

source_name: quiescent 2091 Myc ChIP

tag: quiescent 2091 Myc ChIP


title: Fat line chickens, biological rep5


title: 2091 mock ChIP vs. 4 hours serum stimulated 2091 Myc ChIP set 1


title: Genotype: Steptoe - rep1

description: Steptoe, 7 day old seedling (first leaf unfolded), rep 1


title: Lean line chickens, biological rep5

source_name: lean line chicken adipose tissue at 7-week of age


title: 2091 mock ChIP vs quiescent 2091 Myc ChIP set 1


title: Lean line chickens, biological rep3


title: HeLa mock vs. HeLa Myc ChIP set 2

description: HeLa mock vs. HeLa Myc ChIP

source_name: HeLa mock ChIP

tag: HeLa mock ChIP

source_name: HeLa Myc ChIP

tag: HeLa Myc ChIP


title: XLMR patient (2007090709a)


title: Lean line chickens, biological rep4


title: HeLa mock vs. HeLa Myc ChIP set 4

description: HeLa mock vs. HeLa Myc ChIP


title: Fat line chickens, biological rep1


title: Lean line chickens, biological rep2


title: Lean line chickens, biological rep1


title: HeLa mock vs. HeLa Myc ChIP set 3

description: HeLa mock vs. HeLa Myc ChIP


title: HeLa mock vs. HeLa Myc ChIP set 1

description: HeLa mock vs. HeLa Myc ChIP


title: Fat line chickens, biological rep3


title: EC20_AS_Q2_pool_6-1

status: Public on May 25 2008

city: Santa Clara

first: Thomas

middle: R

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

description: 5' and 3' RACE reactions were performed using using the BD SMARTTM RACE cDNA amplification kit (BD Clontech Cat. No.634914) following the manufacturer's instructions. RACE oligonucleotides were designed with primer3(http://frodo.wi.mit.edu/cgi-bin/primer3/primer3.cgi) with the following parameters: 23 <= primer size <= 27, optimal size = 25, 68oC <= primer Tm <= 72oC, optimal Tm = 70oC,50% = primer GC percentage = 70%.

hyb_protocol: The labeled products were used directly for hybridization to Affymetrix Chromosome 21/22 2.0R Array for 18 h at 450C in a 3 M tetramethyl ammonium chloride/1x MES-based solution containing 100ug/mL Herring Sperm DNA, 0.02% Triton and 30pM of biotinylated control oligo B2 (Affymetrix). All reagents were from Invitrogen, except where noted otherwise.

scan_protocol: Standard Affymetrix protocols

data_processing: The maps of probe intensities versus the genomic positions were generated using Tiling array Software(TAS; http://www.affymetrix.com/support/developer/downloads/TilingArrayTools/index.affx).The graphs were generated without smoothing and median scaling. Each value on the graph represents intensity of the perfect match (PM) probe minus the intensity of the cognate mismatch (MM) probe. The coordinates of the probe always represent the "left" genomic coordinate of a 25-mer.All data is in the coordinates of the hs.NCBIv35 version of the human genome. To minimize the number of falsely positive probes arising from cross-hybridization on the tiling array, we discard all positive probes having more than one perfect hit without gap in the whole genome. RACEfrags were built using a 99.7% percentile in the probe intensity value as a threshold. Two probes are included in the same RACEfrag if they are less than 25 nucleotides away (maxgap), and the minimum length of a RACEfrag (minrun) is 25 nucleotides.

label: Affymetrix DNA labeling reagent (#900542).

molecule: polyA RNA

source_name: Brain

label_protocol: The pooled amplicons were then fragmented to ~ 50-100 nucleotides using DNAse I (Epicenter) at concentration of 0.00625U/ug of DNA for 8 minutes at 37oC followed by boiling for 10 min and cooling on ice. The fragmented amplicons were labeled in the following conditions: 1X terminal transferase(TdT) reaction buffer (Roche); 2.5mM CoCl2, DNA labeling reagent (DLR; Affymetrix; 1.125nmol per 1ug of fragmented DNA) and 200 units of recombinant TdT (Roche) for 3 hours at 37oC

extract_protocol: The products of RACE PCR reactions were pooled and purified by ethanol precipitation.

tag: The sample characteristics which is specific to each pool is detailed in http://genome.imim.es/datasets/racearrays2007


title: EC20_AS_Q2_pool_6-3

source_name: Heart


title: EC20_AS_Q2_pool_4-12

source_name: Placenta


title: PI_20_AS_Q1_pool_2_43

data_processing: The maps of probe intensities versus the genomic positions were generated using Tiling array Software(TAS; http://www.affymetrix.com/support/developer/downloads/TilingArrayTools/index.affx).The graphs were generated without smoothing and median scaling. Each value on the graph represents intensity of the perfect match (PM) probe minus the intensity of the cognate mismatch (MM) probe. The coordinates of the probe always represent the ”left” genomic coordinate of a 25-mer.All data is in the coordinates of the hs.NCBIv35 version of the human genome. To minimize the number of falsely positive probes arising from cross-hybridization on the tiling array, we discard all positive probes having more than one perfect hit without gap in the whole genome. RACEfrags were built using a 99.7% percentile in the probe intensity value as a threshold. Two probes are included in the same RACEfrag if they are less than 25 nucleotides away (maxgap), and the minimum length of a RACEfrag (minrun) is 25 nucleotides.

source_name: Hep G2


title: EC20_AS_Q2_pool_5-6

source_name: Colon


title: EC20_AS_Q2_pool_6-2

source_name: Kidney


title: EC20_AS_Q2_pool_5-5

source_name: Liver


title: PI_20_AS_Q1_pool_2_39

source_name: Fetal Heart


title: EC20_AS_Q2_pool_6-4

source_name: Spleen


title: EC20_AS_Q2_pool_6-5


title: EC20_AS_Q2_pool_5-12


title: EC20_AS_Q2_pool_5-3


title: EC20_AS_Q2_pool_6-6


title: EC20_AS_Q2_pool_5-1


title: PI_20_AS_Q1_pool_2_46

source_name: Hela S3 cells


title: EC20_AS_Q2_pool_5-11

source_name: Testis


title: EC20_AS_Q2_pool_5-9

source_name: Lung


title: PI_20_AS_Q1_pool_2_40

source_name: Fetal Lung


title: EC20_AS_Q2_pool_5-10

source_name: Stomach


title: EC20_AS_Q2_pool_5-8

source_name: Muscle


title: EC20_AS_Q2_pool_5-7

source_name: Small Intestine


title: PI_20_AS_Q1_pool_2_44


title: EC20_AS_Q2_pool_5-2


title: PI_20_AS_Q1_pool_2_45


title: PI_20_AS_Q1_pool_2_42

source_name: Fetus Whole


title: PI_20_AS_Q1_pool_2_47


title: EC20_AS_Q2_pool_5-4


title: PI_20_AS_Q1_pool_2_41

source_name: Fetal Thymus


title: EC20_AS_Q2_pool_4-11


title: PI_20_AS_Q1_pool_2_38

source_name: Fetal Adrenal Gland


title: PI_20_AS_Q1_pool_2_36

source_name: Tongue


title: PI_20_AS_Q1_pool_2_37

source_name: Tonsil


title: EC20_AS_Q2_pool_4-10


title: PI_20_AS_Q1_pool_2_35

source_name: Spinal Cord


title: EC20_AS_Q2_pool_4-5


title: PI_20_AS_Q1_pool_2_33

source_name: Epididymus


title: PI_20_AS_Q1_pool_2_32

source_name: Brain Hypothalamus


title: PI_20_AS_Q1_pool_2_30

source_name: Brain Frontal lob


title: PI_20_AS_Q1_pool_2_34

source_name: Lymph Node


title: EC20_AS_Q2_pool_4-9


title: PI_20_AS_Q1_pool_2_31

source_name: Brain Hippocampus


title: EC20_AS_Q2_pool_4-6

source_name: Colon


title: PI_20_AS_Q1_pool_2_29

source_name: Bladder


title: PI_20_AS_Q1_pool_2_26

source_name: Brain Cerebelum


title: EC20_AS_Q2_pool_4-2

source_name: Kidney


title: PI_20_AS_Q1_pool_2_28

source_name: Uterus


title: EC20_AS_Q2_pool_3-11

source_name: Testis


title: EC20_AS_Q2_pool_4-8

source_name: Muscle


title: EC20_AS_Q2_pool_4-3

source_name: Heart


title: 86_2209.2E.R087U, Experimental replicate 2

description: Data was collected from the hypocotyl regions of Soybean plants at different time points

data_processing: The data were analyzed with RMA suite from R package version 2.4.0. Background correction was using RMA followed by quantile normalization and data was summarized using median polish method

source_name: Soybean cultivar RIL 087 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 087

tag: Tissue/Cell Type


title: EC20_AS_Q2_pool_4-7

source_name: Small Intestine


title: EC20_AS_Q2_pool_4-4

source_name: Spleen


title: PI_20_AS_Q1_pool_2_25

source_name: Adrenal Gland


title: EC20_AS_Q2_pool_4-1

source_name: Brain


title: PI_20_AS_Q1_pool_2_27

source_name: Pituitary Gland


title: EC20_AS_Q2_pool_3-10

source_name: Stomach


title: EC20_AS_Q2_pool_3-7


title: EC20_AS_Q2_pool_3-12

source_name: Placenta


title: PI_20_AS_Q1_pool_2_24

source_name: Salivary Gland


title: EC20_AS_Q2_pool_3-8


title: PI_20_AS_Q1_pool_2_23

source_name: Ovary


title: PI_20_AS_Q1_pool_2_21

source_name: Prostate


title: PI_20_AS_Q1_pool_2_18

source_name: Thymus


title: PI_20_AS_Q1_pool_2_22

source_name: Thyroid


title: EC20_AS_Q2_pool_3-9

source_name: Lung


title: PI_20_AS_Q1_pool_2_20

source_name: Mammary Gland


title: EC20_AS_Q2_pool_3-2

source_name: Kidney


title: EC20_AS_Q2_pool_3-5

source_name: Liver


title: PI_20_AS_Q1_pool_2_15

source_name: Fetal Liver


title: EC20_AS_Q2_pool_3-6

source_name: Colon


title: EC20_AS_Q2_pool_3-4

source_name: Spleen


title: EC20_AS_Q2_pool_3-1


title: PI_20_AS_Q1_pool_2_13

source_name: Skin


title: PI_20_AS_Q1_pool_2_12


title: EC20_AS_Q2_pool_2-11

source_name: Testis


title: PI_20_AS_Q1_pool_2_17

source_name: Fetal Spleen


title: PI_20_AS_Q1_pool_2_16

source_name: Fetal Kidney


title: EC20_AS_Q2_pool_2-9


title: EC20_AS_Q2_pool_2-12

source_name: Placenta


title: PI_20_AS_Q1_pool_2_11


title: PI_20_AS_Q1_pool_2_19

source_name: Pancreas


title: EC20_AS_Q2_pool_3-3

source_name: Heart


title: EC20_AS_Q2_pool_2-10

source_name: Stomach


title: PI_20_AS_Q1_pool_2_14

source_name: Fetal Brain


title: EC20_AS_Q2_pool_2-8

source_name: Muscle


title: PI_20_AS_Q1_pool_2_9

source_name: Lung


title: EC20_AS_Q2_pool_2-7

source_name: Small Intestine


title: PI_20_AS_Q1_pool_2_8


title: EC20_AS_Q2_pool_2-5


title: PI_20_AS_Q1_pool_2_10


title: EC20_AS_Q2_pool_10-12


title: PI_20_AS_Q1_pool_2_4


title: PI_20_AS_Q1_pool_2_5


title: PI_20_AS_Q1_pool_2_6


title: EC20_AS_Q2_pool_2-1

source_name: Brain


title: EC20_AS_Q2_pool_2-6


title: EC20_AS_Q2_pool_2-4


title: EC20_AS_Q2_pool_10-11


title: PI_20_AS_Q3_Pool_16

source_name: a pool of polyA+ RNAs from 12 human tissues brain, heart, kidney, spleen, liver, colon, small intestine, muscle, lung, stomach, testis, placenta


title: PI_20_AS_Q1_pool_2_1


title: EC20_AS_Q2_pool_10-9


title: PI_20_AS_Q1_pool_2_7


title: EC20_AS_Q2_pool_10-10


title: PI_20_AS_Q3_Pool_15


title: EC20_AS_Q2_pool_2-2

source_name: Kidney


title: EC20_AS_Q2_pool_10-6

source_name: Colon


title: EC20_AS_Q2_pool_10-8


title: PI_20_AS_Q3_Pool_14


title: PI_20_AS_Q3_Pool_13


title: PI_20_AS_Q1_pool_2_2


title: EC20_AS_Q2_pool_10-7


title: EC20_AS_Q2_pool_2-3


title: EC20_AS_Q2_pool_10-5

source_name: Liver


title: PI_20_AS_Q1_pool_2_3


title: PI_20_AS_Q3_Pool_12


title: PI_20_AS_Q3_Pool_11


title: EC20_AS_Q2_pool_10-4

source_name: Spleen


title: EC20_AS_Q2_pool_10-3


title: PI_20_AS_Q3_Pool_9


title: EC20_AS_Q2_pool_10-1


title: PI_20_AS_Q3_Pool_6


title: PI_20_AS_Q3_Pool_10


title: PI_20_AS_Q3_Pool_8


title: EC20_AS_Q2_pool_1-11

source_name: Testis


title: PI_20_AS_Q3_Pool_3


title: PI_20_AS_Q3_Pool_5


title: EC20_AS_Q2_pool_10-2


title: PI_20_AS_Q3_Pool_1


title: PI_20_AS_Q3_Pool_2


title: PI_20_AS_Q3_Pool_4


title: EC20_AS_Q2_pool_1-10


title: EC20_AS_Q2_pool_1-5


title: EC20_AS_Q2_pool_1-8


title: PI_20_AS_Q3_Pool_7


title: PI_20_AS_Q1_pool_1_47


title: EC20_AS_Q2_pool_1-7


title: EC20_AS_Q2_pool_1-9


title: EC20_AS_Q2_pool_1-12


title: EC20_AS_Q2_pool_1-6


title: EC20_AS_Q2_pool_1-2


title: PI_20_AS_Q1_pool_1_46

source_name: Hela S3 cells


title: EC20_AS_Q2_pool_1-3


title: PI_20_AS_Q1_pool_1_42

source_name: Fetus Whole


title: PI_20_AS_Q1_pool_1_43

source_name: Hep G2


title: PI_20_AS_Q1_pool_1_44


title: PI_20_AS_Q1_pool_1_45


title: EC20_AS_Q2_pool_9-12

source_name: Placenta


title: EC20_AS_Q2_pool_1-1


title: EC20_AS_Q2_pool_1-4


title: EC20_AS_Q2_pool_9-10


title: PI_20_AS_Q1_pool_1_41

source_name: Fetal Thymus


title: PI_20_AS_Q1_pool_1_39

source_name: Fetal Heart


title: EC20_AS_Q2_pool_9-11


title: PI_20_AS_Q1_pool_1_38

source_name: Fetal Adrenal Gland


title: 5_1277.1G.R176U, Experimental replicate 1

source_name: Soybean cultivar RIL 176 - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: Timepoint: NA

tag: cultivar - RIL 176


title: PI_20_AS_Q1_pool_1_40

source_name: Fetal Lung


title: EC20_AS_Q2_pool_9-8

source_name: Muscle