title: GM17216

description: Basal gene expression level of lymphoblastoid cell line GM17216.

source_name: Lymphoblastoid cell line GM17216


title: GM17219

status: Public on Jul 24 2010

type: RNA

city: Rochester

first: Liewei

last: Wang

state: MN

address: 200 First street SW

department: Molecular Pharmacology and Experimental Therapeutics

country: USA

institute: Mayo Clinic

description: Basal gene expression level of lymphoblastoid cell line GM17219.

hyb_protocol: The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.

scan_protocol: The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

data_processing: The data were analyzed with Agilent Gene Spring GX 7.3 version using Affymetrix default analysis settings and GC-RMA as the normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoblastoid cell line GM17219

label_protocol: Labeling was performed according to the Affymetrix Gene Chip technical manual.

growth_protocol: LCLs were cultured in RPMI 1640 medium supplemented with 15% heat-inactivated Fetal Bovine Serum (FBS). According to the protocol from the Coriell website (http://ccr.coriell.org/sections/support/global/lymphoblastoid.aspx?pgid=213), LCLs were maintained at a density of 2-8 × 10^5 cells/ml, and were split or re-fed with fresh medium every three days, depending on the growth status of each cell line.

extract_protocol: Total RNA was extracted from each of the cell lines using Qiagen RNeasy Mini kits (QIAGEN, Inc.).  RNA quality was tested using an Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment was used.

tag: ethnic group

value: CA Caucasian-American

tag: cell line (coriell id)

tag: wei id

tag: cell type

value: EBV-transformed lymphoblastoid cells


title: GM17220

description: Basal gene expression level of lymphoblastoid cell line GM17220.

source_name: Lymphoblastoid cell line GM17220


title: GM17120

description: Basal gene expression level of lymphoblastoid cell line GM17120.

source_name: Lymphoblastoid cell line GM17120

value: AA African-American


title: GM17747

description: Basal gene expression level of lymphoblastoid cell line GM17747.

source_name: Lymphoblastoid cell line GM17747

value: HCA Han Chinese-American


title: GM17211

description: Basal gene expression level of lymphoblastoid cell line GM17211.

source_name: Lymphoblastoid cell line GM17211


title: GM17212

description: Basal gene expression level of lymphoblastoid cell line GM17212.

source_name: Lymphoblastoid cell line GM17212


title: GM17117

description: Basal gene expression level of lymphoblastoid cell line GM17117.

source_name: Lymphoblastoid cell line GM17117


title: GM17111

description: Basal gene expression level of lymphoblastoid cell line GM17111.

source_name: Lymphoblastoid cell line GM17111


title: GM17742

description: Basal gene expression level of lymphoblastoid cell line GM17742.

source_name: Lymphoblastoid cell line GM17742


title: GM17217

description: Basal gene expression level of lymphoblastoid cell line GM17217.

source_name: Lymphoblastoid cell line GM17217


title: GM17115

description: Basal gene expression level of lymphoblastoid cell line GM17115.

source_name: Lymphoblastoid cell line GM17115


title: GM17112

description: Basal gene expression level of lymphoblastoid cell line GM17112.

source_name: Lymphoblastoid cell line GM17112


title: GM17227

description: Basal gene expression level of lymphoblastoid cell line GM17227.

source_name: Lymphoblastoid cell line GM17227


title: GM17743

description: Basal gene expression level of lymphoblastoid cell line GM17743.

source_name: Lymphoblastoid cell line GM17743


title: GM17745

description: Basal gene expression level of lymphoblastoid cell line GM17745.

source_name: Lymphoblastoid cell line GM17745


title: GM17214

description: Basal gene expression level of lymphoblastoid cell line GM17214.

source_name: Lymphoblastoid cell line GM17214


title: GM17738

description: Basal gene expression level of lymphoblastoid cell line GM17738.

source_name: Lymphoblastoid cell line GM17738


title: GM17108

description: Basal gene expression level of lymphoblastoid cell line GM17108.

source_name: Lymphoblastoid cell line GM17108


title: GM17744

description: Basal gene expression level of lymphoblastoid cell line GM17744.

source_name: Lymphoblastoid cell line GM17744


title: GM17113

description: Basal gene expression level of lymphoblastoid cell line GM17113.

source_name: Lymphoblastoid cell line GM17113


title: GM17109

description: Basal gene expression level of lymphoblastoid cell line GM17109.

source_name: Lymphoblastoid cell line GM17109


title: GM17114

description: Basal gene expression level of lymphoblastoid cell line GM17114.

source_name: Lymphoblastoid cell line GM17114


title: GM17741

description: Basal gene expression level of lymphoblastoid cell line GM17741.

source_name: Lymphoblastoid cell line GM17741


title: GM17210

description: Basal gene expression level of lymphoblastoid cell line GM17210.

source_name: Lymphoblastoid cell line GM17210


title: GM17208

description: Basal gene expression level of lymphoblastoid cell line GM17208.

source_name: Lymphoblastoid cell line GM17208


title: GM17106

description: Basal gene expression level of lymphoblastoid cell line GM17106.

source_name: Lymphoblastoid cell line GM17106


title: GM17739

description: Basal gene expression level of lymphoblastoid cell line GM17739.

source_name: Lymphoblastoid cell line GM17739


title: GM17206

description: Basal gene expression level of lymphoblastoid cell line GM17206.

source_name: Lymphoblastoid cell line GM17206


title: GM17735

description: Basal gene expression level of lymphoblastoid cell line GM17735.

source_name: Lymphoblastoid cell line GM17735


title: GM17107

description: Basal gene expression level of lymphoblastoid cell line GM17107.

source_name: Lymphoblastoid cell line GM17107


title: GM17740

description: Basal gene expression level of lymphoblastoid cell line GM17740.

source_name: Lymphoblastoid cell line GM17740


title: GM17737

description: Basal gene expression level of lymphoblastoid cell line GM17737.

source_name: Lymphoblastoid cell line GM17737


title: GM17207

description: Basal gene expression level of lymphoblastoid cell line GM17207.

source_name: Lymphoblastoid cell line GM17207


title: GM17103

description: Basal gene expression level of lymphoblastoid cell line GM17103.

source_name: Lymphoblastoid cell line GM17103


title: GM17733

description: Basal gene expression level of lymphoblastoid cell line GM17733.

source_name: Lymphoblastoid cell line GM17733


title: GM17202

description: Basal gene expression level of lymphoblastoid cell line GM17202.

source_name: Lymphoblastoid cell line GM17202


title: GM17205

description: Basal gene expression level of lymphoblastoid cell line GM17205.

source_name: Lymphoblastoid cell line GM17205


title: Laval_Laval_hybrid individual_4 (SAMPLE 96)

status: Public on Jul 01 2010

city: Québec

first: Berenice

last: BOUGAS

state: QC

address: 1030 avenue de la médecine, IBIS, Pavillon Marchand

department: Biology

country: Canada

institute: Laval university

description:
SAMPLE 96
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.

hyb_protocol: Microarray were hybridized using Cy3/Al647 dyes (Genisphere) as detailed in http://web.uvic.ca/grasp/microarray/protocols/Genisphere_Array_50_Protocol_Revised_v.5.pdf

scan_protocol: Microarrays were scanned using a ScanArray scanner (Packard BioScience). Spots were localized and quantified with the QuantArray 3.0 software, using the histogram quantification method and keeping the mean value of intensity for each spot.

data_processing: Data were exported in text format and were analysed using a mixed model ANOVA and the R/MAANOVA package (Kerr and Churchill 2000)

organism: Salvelinus fontinalis

source_name: Frozen individual in toto

label_protocol: For each sample, 12µg total RNA was retro-transcribed and the cDNA samples labelled using Genisphere 3DNA Array 50 Kit, Invitrogen’s Superscript II retro-transcriptase and Cyanine3 and Alexa 647 fluorescent dyes (Genisphere), following the procedures at http://web.uvic.ca/cbr/grasp/ (Genisphere Array 50 Protocol).

growth_protocol: Whole individuals were stored at -80°C prior to any sampling

extract_protocol: Total RNA was extracted with PureLink TM Micro-to-Midi Total RNA Purification System Kit and then treated using DNase I, Amplification Grade (1 unit/μl) (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Total RNA were further purified by ultra-centrifugation using microcon (Millipore) spin columns. The 48 deep-frozen individuals were extracted in toto to obtain the expression of whole transcriptome. Quality and integrity of the total RNA was controlled with an Experion Automated Electrophoresis Station and RNA HighSens Chips (Biorad, Hercules, CA). Total RNA was stored in pure water supplemented with Superase-In™ RNase Inhibitor (Ambion) at -80°C.

treatment_protocol: Samples were treated with DNAse enzyme prior to labeling

tag: common name

value: brook charr

tag: cross

value: Laval*Laval

tag: individual

value: One sexually undifferentiated individual

tag: individual number

tag: developmental stage

value: yolk sac resorption stage

tag: tissue

value: whole individual


title: GM17203

description: Basal gene expression level of lymphoblastoid cell line GM17203.

source_name: Lymphoblastoid cell line GM17203


title: GM17736

description: Basal gene expression level of lymphoblastoid cell line GM17736.

source_name: Lymphoblastoid cell line GM17736


title: GM17734

description: Basal gene expression level of lymphoblastoid cell line GM17734.

source_name: Lymphoblastoid cell line GM17734


title: Rupert_Laval_hybrid individual_9 (SAMPLE 95)

description:
SAMPLE 95
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.

value: Rupert*Laval


title: GM17104

description: Basal gene expression level of lymphoblastoid cell line GM17104.

source_name: Lymphoblastoid cell line GM17104


title: GM17105

description: Basal gene expression level of lymphoblastoid cell line GM17105.

source_name: Lymphoblastoid cell line GM17105


title: Rupert_Rupert_hybrid individual_6 (SAMPLE 90)

description:
SAMPLE 90
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.

value: Rupert*Rupert


title: Domestic_Domestic_hybrid individual_9 (SAMPLE 93)

description:
SAMPLE 93
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.

value: Domestic*Domestic


title: GM17201

description: Basal gene expression level of lymphoblastoid cell line GM17201.

source_name: Lymphoblastoid cell line GM17201


title: Laval_Domestic_hybrid individual_7 (SAMPLE 92)

description:
SAMPLE 92
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.

value: Laval*Domestic


title: Laval_Laval_hybrid individual_6 (SAMPLE 85)

description:
SAMPLE 85
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_6 (SAMPLE 91)

description:
SAMPLE 91
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: GM17102

description: Basal gene expression level of lymphoblastoid cell line GM17102.

source_name: Lymphoblastoid cell line GM17102


title: Rupert_Laval_hybrid individual_7 (SAMPLE 86)

description:
SAMPLE 86
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_3 (SAMPLE 88)

description:
SAMPLE 88
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_6 (SAMPLE 94)

description:
SAMPLE 94
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_4 (SAMPLE 87)

description:
SAMPLE 87
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_2 (SAMPLE 83)

description:
SAMPLE 83
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_10 (SAMPLE 89)

description:
SAMPLE 89
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_3 (SAMPLE 78)

description:
SAMPLE 78
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_6 (SAMPLE 80)

description:
SAMPLE 80
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_2 (SAMPLE 81)

description:
SAMPLE 81
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: GM17222

description: Basal gene expression level of lymphoblastoid cell line GM17222.

source_name: Lymphoblastoid cell line GM17222


title: Laval_Domestic_hybrid individual_4 (SAMPLE 79)

description:
SAMPLE 79
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_5 (SAMPLE 75)

description:
SAMPLE 75
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_7 (SAMPLE 71)

description:
SAMPLE 71
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_2 (SAMPLE 72)

description:
SAMPLE 72
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_5 (SAMPLE 84)

description:
SAMPLE 84
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_3 (SAMPLE 82)

description:
SAMPLE 82
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_3 (SAMPLE 69)

description:
SAMPLE 69
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_3 (SAMPLE 74)

description:
SAMPLE 74
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_4 (SAMPLE 73)

description:
SAMPLE 73
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_8 (SAMPLE 68)

description:
SAMPLE 68
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_8 (SAMPLE 76)

description:
SAMPLE 76
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_5 (SAMPLE 77)

description:
SAMPLE 77
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_7 (SAMPLE 70)

description:
SAMPLE 70
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_4 (SAMPLE 67)

description:
SAMPLE 67
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_4 (SAMPLE 64)

description:
SAMPLE 64
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_1 (SAMPLE 60)

description:
SAMPLE 60
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_4 (SAMPLE 61)

description:
SAMPLE 61
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.

value: Domestic*Rupert


title: Rupert_Laval_hybrid individual_7 (SAMPLE 59)

description:
SAMPLE 59
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_6 (SAMPLE 55)

description:
SAMPLE 55
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_3 (SAMPLE 57)

description:
SAMPLE 57
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_1 (SAMPLE 50)

description:
SAMPLE 50
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_6 (SAMPLE 62)

description:
SAMPLE 62
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_1 (SAMPLE 63)

description:
SAMPLE 63
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_1 (SAMPLE 51)

description:
SAMPLE 51
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_2 (SAMPLE 66)

description:
SAMPLE 66
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_6 (SAMPLE 54)

description:
SAMPLE 54
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_9 (SAMPLE 56)

description:
SAMPLE 56
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_9 (SAMPLE 58)

description:
SAMPLE 58
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_10 (SAMPLE 52)

description:
SAMPLE 52
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_5 (SAMPLE 65)

description:
SAMPLE 65
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_6 (SAMPLE 53)

description:
SAMPLE 53
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_8 (SAMPLE 47)

description:
SAMPLE 47
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_8 (SAMPLE 46)

description:
SAMPLE 46
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_3 (SAMPLE 48)

description:
SAMPLE 48
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_5 (SAMPLE 44)

description:
SAMPLE 44
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_8 (SAMPLE 45)

description:
SAMPLE 45
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_5 (SAMPLE 41)

description:
SAMPLE 41
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_2 (SAMPLE 40)

description:
SAMPLE 40
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_3 (SAMPLE 43)

description:
SAMPLE 43
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_2 (SAMPLE 37)

description:
SAMPLE 37
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_10 (SAMPLE 36)

description:
SAMPLE 36
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_2 (SAMPLE 35)

description:
SAMPLE 35
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_8 (SAMPLE 38)

description:
SAMPLE 38
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_6 (SAMPLE 49)

description:
SAMPLE 49
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_8 (SAMPLE 42)

description:
SAMPLE 42
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_2 (SAMPLE 34)

description:
SAMPLE 34
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_8 (SAMPLE 39)

description:
SAMPLE 39
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_9 (SAMPLE 29)

description:
SAMPLE 29
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_6 (SAMPLE 31)

description:
SAMPLE 31
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Laval_hybrid individual_9 (SAMPLE 28)

description:
SAMPLE 28
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_8 (SAMPLE 32)

description:
SAMPLE 32
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_8 (SAMPLE 33)

description:
SAMPLE 33
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_10 (SAMPLE 27)

description:
SAMPLE 27
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_10 (SAMPLE 25)

description:
SAMPLE 25
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_6 (SAMPLE 30)

description:
SAMPLE 30
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_9 (SAMPLE 22)

description:
SAMPLE 22
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_1 (SAMPLE 20)

description:
SAMPLE 20
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_5 (SAMPLE 24)

description:
SAMPLE 24
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_7 (SAMPLE 23)

description:
SAMPLE 23
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_4 (SAMPLE 21)

description:
SAMPLE 21
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_4 (SAMPLE 16)

description:
SAMPLE 16
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_3 (SAMPLE 18)

description:
SAMPLE 18
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_9 (SAMPLE 15)

description:
SAMPLE 15
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Domestic_hybrid individual_2 (SAMPLE 17)

description:
SAMPLE 17
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_5 (SAMPLE 13)

description:
SAMPLE 13
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_7 (SAMPLE 14)

description:
SAMPLE 14
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_10 (SAMPLE 10)

description:
SAMPLE 10
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Laval_Domestic_hybrid individual_10 (SAMPLE 26)

description:
SAMPLE 26
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_4 (SAMPLE 12)

description:
SAMPLE 12
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_10 (SAMPLE 19)

description:
SAMPLE 19
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_9 (SAMPLE 11)

description:
SAMPLE 11
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_4 (SAMPLE 2)

description:
SAMPLE 2
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_9 (SAMPLE 6)

description:
SAMPLE 6
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Domestic_Rupert_hybrid individual_3 (SAMPLE 7)

description:
SAMPLE 7
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Laval_hybrid individual_2 (SAMPLE 4)

description:
SAMPLE 4
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_7 (SAMPLE 5)

description:
SAMPLE 5
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_1 (SAMPLE 9)

description:
SAMPLE 9
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_5 (SAMPLE 8)

description:
SAMPLE 8
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_5 (SAMPLE 1)

description:
SAMPLE 1
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: Rupert_Rupert_hybrid individual_4 (SAMPLE 3)

description:
SAMPLE 3
Technical replicate hybridized on 2 distinct slides (i.e., each individual was used two times), each slide representing a dual channel hybridization.


title: cDNA array winter+common reference set4

status: Public on Jun 01 2010

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

country: China

institute: College of life sciences, Peking University

description: Comparison of gene expression profiles of +7 DPA wild-type in winter (February) and a four-season mix common reference RNA sample.

hyb_protocol: Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed with 30 uL hybridization solution (50% formamide, 1x hybridization buffer; Amersham Biosciences). DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized at 42℃ overnight and washed with two consecutive solutions (0.2% SDS, 2x SSC at 42℃ for 5 min, and 0.2x SSC for 5 min) at room temperature.

scan_protocol: Arrays were scanned with a LuxScanTM 10K/A scanner (CapitalBio), and obtained images were analyzed with GenePix 4.0(Axon).

data_processing: Signal intensities for each spot were calculated by subtracting local background (based on the median intensity of the area surrounding each spot) from total intensities. Raw data was global scaled making the average signal intensity of arrays was equal, allowing comparison among chips. Weak spots (signal intensity smaller than 400 in all samples) were removed from further analysis and negative value was converted to 10. The preprocessed data was loaded into MAANOVA under R environment for Lowess normalization within each slide, and multiple testing by fitting fixed effects ANOVA model[4]. Microarray spots with FDR-corrected P values <0.001 in the F-test and expression between the two samples differed by 2-fold from their average expression across the technical and biological replicates of the samples were considered to be significant.

organism: Gossypium hirsutum

source_name: +7 DPA wide-type cotton ovule obtained in winter (February)

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine's linear RNA amplification method and subsequent enzymatic reaction. In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 10 ug total RNA using the cDNA synthesis system according to the manufacturer's protocol (TaKaRa). A T7-oligo(dT) primer (5'-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT-3') was used instead of the poly-T primer provided in the kit. After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR purification kit (Qiagen) and eluted with 60 uL elution buffer. One-half of the eluted double-stranded cDNA products were vacuum evaporated to 8 uL and subjected to 20 uL in vitro transcription reactions at 37℃ for 3 h using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNeasy mini kit (Qiagen). Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 ug amplified RNA was mixed with 2 ug random hexamers, denatured at 70℃ for 5 min, and cooled on ice. Then, 4 uL of first-strand buffer, 2 uL of 0.1 M DTT, 1 uL 10 mM dNTP, and 1.5 uL SuperScript II (Invitrogen) were added. The mixtures were incubated at 25℃ for 10 min, then at 42℃ for 60 min. The cDNA products were purified using a PCR purification kit (Qiagen) and vacuum evaporated to 10 uL. Klenow enzyme (1 uL; TaKaRa) was then added, and the reaction was performed at 37℃ for 60 min.

extract_protocol: Labeled cDNA was purified with a PCR purification kit (Qiagen) and resuspended in elution buffer.

tag: age

value: +7 DPA wide-type

value: cotton ovules

tag: season

value: winter (February)

source_name: common reference

value: +7 DPA

value: wide-type cotton ovules (mix)

value: all four seasons (May, August, November, February)


title: cDNA array winter+common reference set2


title: cDNA array winter+common reference set3 (dye swap)


title: cDNA array winter+common reference set2 (dye swap)


title: CCPE Replicate 1

status: Public on Jun 23 2010

city: Boston

first: Zhijian

last: Gao

state: MA

address: Longwood 221

institute: BWH, Harvard Medical School

hyb_protocol: In all, 1.5μg of dye-labeled aRNA of each RNA preparation was fragmented and combined with hybridization controls using in situ Hybridization Kit Plus (Agilent Technologies, Santa Clara, CA). The GeneChips were hybridized overnight at 45℃ in a GeneMachine Hyb4 slide hybridization machine (Genomic Solutions, Ann Arbor, MI) and subsequently washed as recommended by the manufacturer.

scan_protocol: Scanning was performed on a ScanArray 4000XL Microarray Analysis System, and quantified using ScanArray Express (Perkin Elmer, Downers Grove, IL).

data_processing: Normalized sample to control ratios were used for analysis.  Dye swap comparisons were performed to assure that no bias was introduced by the hybridization process.

source_name: untreated SKOV-3 ovarian cancer cell line

label_protocol: Dye-labeled aRNA was prepared as described in the Amino Allyl MessageAmp II aRNA Amplification kit Manual (Ambion Inc., Austin, TX). Briefly, 1 μg of purified total RNA was reverse transcribed to generate double-stranded cDNA using T7 Oligo primer and reverse transcriptase. Following second-strand cDNA synthesis and purification, biotin-labeled antisense RNA (aRNA) was modified with amino allyl UTP (aaUTP) by in vitro transcription and coupled with Cy3 and Cy5.

growth_protocol: SKOV-3 cells were were maintained in a 1:1 mixture of MM199 and MCDB 105 (Sigma, St. Louis, MO) medium supplemented with 10%FBS

extract_protocol: Total RNAs were extracted and purified from the confluent cultures using the RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: SKOV-3 cells were without C-CPE (5μg/ml) for 72 hours

tag: cell line

source_name: SKOV-3 ovarian cancer cell line treated with C-CPE

treatment_protocol: SKOV-3 cells were treated with C-CPE (5μg/ml) for 72 hours


title: cDNA array winter+common reference set4 (dye swap)


title: CCPE Replicate 3


title: CCPE Replicate 2


title: cDNA array winter+common reference set1


title: cDNA array winter+common reference set3


title: cDNA array autumn+common reference set2

description: Comparison of gene expression profiles of +7 DPA wild-type in autumn (November) and a four-season mix common reference RNA sample.

source_name: +7 DPA wide-type cotton ovule obtained in autumn (November)

value: autumn (November)


title: cDNA array autumn+common reference set3 (dye swap)


title: cDNA array autumn+common reference set4 (dye swap)


title: cDNA array autumn+common reference set1 (dye swap)


title: cDNA array winter+common reference set1 (dye swap)


title: cDNA array autumn+common reference set2 (dye swap)


title: cDNA array autumn+common reference set4


title: cDNA array autumn+common reference set3


title: cDNA array summer+common reference set4 (dye swap)

description: Comparison of gene expression profiles of +7 DPA wild-type in summer (August) and a four-season mix common reference RNA sample.

source_name: +7 DPA wide-type cotton ovule obtained in summer (August)

value: +10 DPA wide-type

value: summer (August)


title: cDNA array autumn+common reference set1


title: cDNA array summer+common reference set2


title: cDNA array summer+common reference set3 (dye swap)

source_name: +10 DPA wide-type cotton ovule obtained in summer (August)


title: cDNA array summer+common reference set3


title: cDNA array summer+common reference set1 (dye swap)


title: cDNA array summer+common reference set4


title: cDNA array spring+common reference set2 (dye swap)

description: Comparison of gene expression profiles of +7 DPA wild-type in spring (May) and a four-season mix common reference RNA sample.

source_name: +7 DPA wide-type cotton ovule obtained in spring (May)

value: spring (May)


title: cDNA array spring+common reference set3 (dye swap)


title: cDNA array spring+common reference set1 (dye swap)

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine's linear RNA amplification method and subsequent enzymatic reaction. In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 10 ¦Ìg total RNA using the cDNA synthesis system according to the manufacturer's protocol (TaKaRa). A T7-oligo(dT) primer (5'-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT-3') was used instead of the poly-T primer provided in the kit. After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR purification kit (Qiagen) and eluted with 60 uL elution buffer. One-half of the eluted double-stranded cDNA products were vacuum evaporated to 8 uL and subjected to 20-uL in vitro transcription reactions at 37℃ for 3 h using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNeasy mini kit (Qiagen). Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 ¦Ìg amplified RNA was mixed with 2 ¦Ìg random hexamers, denatured at 70℃ for 5 min, and cooled on ice. Then, 4 uL of first-strand buffer, 2 uL of 0.1 M DTT, 1 uL 10 mM dNTP, and 1.5 uL SuperScript II (Invitrogen) were added. The mixtures were incubated at 25℃ for 10 min, then at 42℃ for 60 min. The cDNA products were purified using a PCR purification kit (Qiagen) and vacuum evaporated to 10 uL. Klenow enzyme (1 uL; TaKaRa) was then added, and the reaction was performed at 37℃ for 60 min.


title: cDNA array summer+common reference set2 (dye swap)


title: cDNA array summer+common reference set1


title: cDNA array spring+common reference set2


title: RNA Pol II ChIP-chip

status: Public on May 29 2010

type: genomic

city: Los Angeles

first: matteo

last: Pellegrini

state: CA

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

description: Pol II ChIP vs DNA

hyb_protocol: Whole Genome Tiling Array was hybridized for 16 hrs, washed, and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix scanner G7

data_processing: Quantile Normalization, bar file contains log2 of quantile normalized probe-level hybridization signal

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: RNA Pol II

label_protocol: The sample was 3'-end-labelled with dd-UTP (Roche) by the terminal transferace (TdT, Roche) reaction for 1.5 h at 37 degrees C.

growth_protocol: Plants were grown under 24hr light on soil

extract_protocol: sample was prepared by ChIP using an antibody against Pol II

value: shoots

value: 10-14 day seedlings

tag: antibody vendor

value: Abcam

tag: catalog number

tag: lot number


title: Input DNA

description: Pol II ChIP vs DNA

source_name: Input DNA

tag: sample type

value: input DNA


title: cDNA array spring+common reference set1


title: cDNA array spring+common reference set4


title: cDNA array spring+common reference set4 (dye swap)


title: Parental Liver Pool (n=176) vs. 118022

status: Public on May 25 2010

city: Seattle

first: Wan-Lin

last: Su

state: WA

address: 401 Terry Ave N

institute: Rosetta Inpharmatics (a wholly owned subsidiary of Merck & Co., Inc.)

description: Expression profiling of liver tissue from 22 different inbred strains representing both male and female mice.  All mice were reared at Jackson Laboratories in Bar Harbor, ME and shipped to Jackson Laboratories in Sacramento, CA (JAX West) at 7 weeks of age.  All mice were maintained on a 12h light-dark cycle and fed ad libitum.  At 20 weeks of age all mice were euthanized and liver tissues were collected and flash frozen in liquid nitrogen and stored at -80 degrees C prior to RNA isolation.  All procedures of housing and treatment of animals were performed in accordance with IACUC regulations.

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. INTENSITY1 and INTENSITY2 columns represents the raw data for each sample that we obtained from combining two hybridizations per sample.

organism: Mus musculus

source_name: Liver

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

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: reference

value: Parental Liver Pool (n=176)

tag: strain

value: SM/J

tag: Sex

value: M


title: Parental Liver Pool (n=176) vs. 119022

value: SWR/J


title: Parental Liver Pool (n=176) vs. 119014


title: Parental Liver Pool (n=176) vs. 118024


title: Parental Liver Pool (n=176) vs. 118019


title: Parental Liver Pool (n=176) vs. 119024


title: Parental Liver Pool (n=176) vs. 119013


title: Parental Liver Pool (n=176) vs. 119018


title: Parental Liver Pool (n=176) vs. 118017


title: Parental Liver Pool (n=176) vs. 119015


title: Parental Liver Pool (n=176) vs. 119009

value: F


title: Parental Liver Pool (n=176) vs. 119017


title: Parental Liver Pool (n=176) vs. 119006


title: Parental Liver Pool (n=176) vs. 119003


title: Parental Liver Pool (n=176) vs. 119011


title: Parental Liver Pool (n=176) vs. 119010


title: Parental Liver Pool (n=176) vs. 119021


title: Parental Liver Pool (n=176) vs. 119012


title: Parental Liver Pool (n=176) vs. 119005


title: Parental Liver Pool (n=176) vs. 119007


title: Parental Liver Pool (n=176) vs. 119004


title: Parental Liver Pool (n=176) vs. 119001


title: Parental Liver Pool (n=176) vs. 118023


title: Parental Liver Pool (n=176) vs. 119020


title: Parental Liver Pool (n=176) vs. 119023


title: Parental Liver Pool (n=176) vs. 119016


title: Parental Liver Pool (n=176) vs. 118014


title: Parental Liver Pool (n=176) vs. 118016


title: Parental Liver Pool (n=176) vs. 118009


title: cDNA array spring+common reference set3

value: +7 DPA wide-type

value: cotton ovules


title: Parental Liver Pool (n=176) vs. 118015


title: Parental Liver Pool (n=176) vs. 118005


title: Parental Liver Pool (n=176) vs. 117023

value: SJL/J


title: Parental Liver Pool (n=176) vs. 118001


title: Parental Liver Pool (n=176) vs. 118012


title: Parental Liver Pool (n=176) vs. 117020


title: Parental Liver Pool (n=176) vs. 118008


title: Parental Liver Pool (n=176) vs. 118011


title: Parental Liver Pool (n=176) vs. 118004


title: Parental Liver Pool (n=176) vs. 117015


title: Parental Liver Pool (n=176) vs. 117019


title: Parental Liver Pool (n=176) vs. 118006


title: Parental Liver Pool (n=176) vs. 118018


title: Parental Liver Pool (n=176) vs. 117016


title: Parental Liver Pool (n=176) vs. 117022


title: Parental Liver Pool (n=176) vs. 117018


title: Parental Liver Pool (n=176) vs. 117012


title: Parental Liver Pool (n=176) vs. 118010


title: Parental Liver Pool (n=176) vs. 118002


title: Parental Liver Pool (n=176) vs. 117013


title: Parental Liver Pool (n=176) vs. 117011


title: Parental Liver Pool (n=176) vs. 117021


title: Parental Liver Pool (n=176) vs. 117014


title: Parental Liver Pool (n=176) vs. 118007


title: Parental Liver Pool (n=176) vs. 118013


title: Parental Liver Pool (n=176) vs. 117008


title: Parental Liver Pool (n=176) vs. 117004


title: Parental Liver Pool (n=176) vs. 117003


title: Parental Liver Pool (n=176) vs. 117006


title: Parental Liver Pool (n=176) vs. 116014

value: PERA/EiJ


title: Parental Liver Pool (n=176) vs. 117005


title: Parental Liver Pool (n=176) vs. 116013


title: Parental Liver Pool (n=176) vs. 116020


title: Parental Liver Pool (n=176) vs. 117002


title: Parental Liver Pool (n=176) vs. 116021


title: Parental Liver Pool (n=176) vs. 116016


title: Parental Liver Pool (n=176) vs. 116008


title: Parental Liver Pool (n=176) vs. 115022

value: NZO/HILtJ


title: Parental Liver Pool (n=176) vs. 116005


title: Parental Liver Pool (n=176) vs. 116011


title: Parental Liver Pool (n=176) vs. 116009


title: Parental Liver Pool (n=176) vs. 116012


title: Parental Liver Pool (n=176) vs. 116006


title: Parental Liver Pool (n=176) vs. 115023


title: Parental Liver Pool (n=176) vs. 115021


title: Parental Liver Pool (n=176) vs. 116007


title: Parental Liver Pool (n=176) vs. 116010


title: Parental Liver Pool (n=176) vs. 116003


title: Parental Liver Pool (n=176) vs. 117009


title: Parental Liver Pool (n=176) vs. 117001


title: Parental Liver Pool (n=176) vs. 116002


title: Parental Liver Pool (n=176) vs. 115024


title: Parental Liver Pool (n=176) vs. 116001


title: Parental Liver Pool (n=176) vs. 115020


title: Parental Liver Pool (n=176) vs. 116004


title: Parental Liver Pool (n=176) vs. 115019


title: Parental Liver Pool (n=176) vs. 115018


title: Parental Liver Pool (n=176) vs. 115016


title: Parental Liver Pool (n=176) vs. 115013


title: Parental Liver Pool (n=176) vs. 115015


title: Parental Liver Pool (n=176) vs. 115017


title: Parental Liver Pool (n=176) vs. 115014


title: Parental Liver Pool (n=176) vs. 115002


title: Parental Liver Pool (n=176) vs. 115003


title: Parental Liver Pool (n=176) vs. 115008


title: Parental Liver Pool (n=176) vs. 115009


title: Parental Liver Pool (n=176) vs. 115001


title: Parental Liver Pool (n=176) vs. 114024

value: NZB/BlNJ


title: Parental Liver Pool (n=176) vs. 115007


title: Parental Liver Pool (n=176) vs. 114018


title: Parental Liver Pool (n=176) vs. 114023


title: Parental Liver Pool (n=176) vs. 114014


title: Parental Liver Pool (n=176) vs. 114017


title: Parental Liver Pool (n=176) vs. 114016


title: Parental Liver Pool (n=176) vs. 114020


title: Parental Liver Pool (n=176) vs. 114013


title: Parental Liver Pool (n=176) vs. 114012


title: Parental Liver Pool (n=176) vs. 114015


title: Parental Liver Pool (n=176) vs. 114022


title: Parental Liver Pool (n=176) vs. 114010


title: Parental Liver Pool (n=176) vs. 114009


title: Parental Liver Pool (n=176) vs. 114001


title: Parental Liver Pool (n=176) vs. 113014

value: NOD/LtJ


title: Parental Liver Pool (n=176) vs. 114004


title: Parental Liver Pool (n=176) vs. 113006


title: Parental Liver Pool (n=176) vs. 113016


title: Parental Liver Pool (n=176) vs. 114006


title: Parental Liver Pool (n=176) vs. 114007


title: Parental Liver Pool (n=176) vs. 114002


title: Parental Liver Pool (n=176) vs. 113021


title: Parental Liver Pool (n=176) vs. 113018


title: Parental Liver Pool (n=176) vs. 113015


title: Parental Liver Pool (n=176) vs. 115004


title: Parental Liver Pool (n=176) vs. 112022

value: LG/J


title: Parental Liver Pool (n=176) vs. 113020


title: Parental Liver Pool (n=176) vs. 113024


title: Parental Liver Pool (n=176) vs. 113017


title: Parental Liver Pool (n=176) vs. 112021


title: Parental Liver Pool (n=176) vs. 113019


title: Parental Liver Pool (n=176) vs. 112023


title: Parental Liver Pool (n=176) vs. 113007


title: Parental Liver Pool (n=176) vs. 113013


title: Parental Liver Pool (n=176) vs. 113003


title: Parental Liver Pool (n=176) vs. 113005


title: Parental Liver Pool (n=176) vs. 113002


title: Parental Liver Pool (n=176) vs. 112019


title: Parental Liver Pool (n=176) vs. 112020


title: Parental Liver Pool (n=176) vs. 112018


title: Parental Liver Pool (n=176) vs. 112017


title: Parental Liver Pool (n=176) vs. 112004


title: Parental Liver Pool (n=176) vs. 112012


title: Parental Liver Pool (n=176) vs. 112013


title: Parental Liver Pool (n=176) vs. 112011


title: Parental Liver Pool (n=176) vs. 112009


title: Parental Liver Pool (n=176) vs. 111016

value: FVB/NJ


title: Parental Liver Pool (n=176) vs. 112003


title: Parental Liver Pool (n=176) vs. 111020


title: Parental Liver Pool (n=176) vs. 111015


title: Parental Liver Pool (n=176) vs. 111017


title: Parental Liver Pool (n=176) vs. 111011


title: Parental Liver Pool (n=176) vs. 111014


title: Parental Liver Pool (n=176) vs. 111024


title: Parental Liver Pool (n=176) vs. 111009


title: Parental Liver Pool (n=176) vs. 111018


title: Parental Liver Pool (n=176) vs. 112002


title: Parental Liver Pool (n=176) vs. 111021


title: Parental Liver Pool (n=176) vs. 111010


title: Parental Liver Pool (n=176) vs. 112008


title: Parental Liver Pool (n=176) vs. 112001


title: Parental Liver Pool (n=176) vs. 111008


title: Parental Liver Pool (n=176) vs. 112014


title: Parental Liver Pool (n=176) vs. 111006


title: Parental Liver Pool (n=176) vs. 111004


title: Parental Liver Pool (n=176) vs. 111002


title: Parental Liver Pool (n=176) vs. 111005


title: Parental Liver Pool (n=176) vs. 111023


title: Parental Liver Pool (n=176) vs. 111001


title: Parental Liver Pool (n=176) vs. 110024


title: Parental Liver Pool (n=176) vs. 110023


title: Parental Liver Pool (n=176) vs. 110020


title: Parental Liver Pool (n=176) vs. 110022


title: Parental Liver Pool (n=176) vs. 110019


title: Parental Liver Pool (n=176) vs. 110016


title: Parental Liver Pool (n=176) vs. 110018


title: Parental Liver Pool (n=176) vs. 110014


title: Parental Liver Pool (n=176) vs. 110009


title: Parental Liver Pool (n=176) vs. 110012


title: Parental Liver Pool (n=176) vs. 110011


title: Parental Liver Pool (n=176) vs. 110008


title: Parental Liver Pool (n=176) vs. 110005


title: Parental Liver Pool (n=176) vs. 110007


title: Parental Liver Pool (n=176) vs. 110015


title: Parental Liver Pool (n=176) vs. 110004


title: Parental Liver Pool (n=176) vs. 110006


title: Parental Liver Pool (n=176) vs. 110013


title: Parental Liver Pool (n=176) vs. 110003


title: Parental Liver Pool (n=176) vs. 122029

value: CZECHII/EiJ


title: Parental Liver Pool (n=176) vs. 110001


title: Parental Liver Pool (n=176) vs. 110002


title: Parental Liver Pool (n=176) vs. 122024


title: Parental Liver Pool (n=176) vs. 122026


title: Parental Liver Pool (n=176) vs. 122028


title: Parental Liver Pool (n=176) vs. 122025


title: Parental Liver Pool (n=176) vs. 122015


title: Parental Liver Pool (n=176) vs. 122013


title: Parental Liver Pool (n=176) vs. 122023


title: Parental Liver Pool (n=176) vs. 110017


title: Parental Liver Pool (n=176) vs. 122016


title: Parental Liver Pool (n=176) vs. 122017


title: Parental Liver Pool (n=176) vs. 122022


title: Parental Liver Pool (n=176) vs. 109017

value: CAST/EiJ


title: Parental Liver Pool (n=176) vs. 109019


title: Parental Liver Pool (n=176) vs. 109023


title: Parental Liver Pool (n=176) vs. 122006


title: Parental Liver Pool (n=176) vs. 122010


title: Parental Liver Pool (n=176) vs. 122011


title: Parental Liver Pool (n=176) vs. 109009


title: Parental Liver Pool (n=176) vs. 109022


title: Parental Liver Pool (n=176) vs. 109005


title: Parental Liver Pool (n=176) vs. 122009


title: Parental Liver Pool (n=176) vs. 109013


title: Parental Liver Pool (n=176) vs. 109024


title: Parental Liver Pool (n=176) vs. 109021


title: Parental Liver Pool (n=176) vs. 109014


title: Parental Liver Pool (n=176) vs. 109010


title: Parental Liver Pool (n=176) vs. 109012


title: Parental Liver Pool (n=176) vs. 109025


title: Parental Liver Pool (n=176) vs. 122012


title: Parental Liver Pool (n=176) vs. 109020


title: Parental Liver Pool (n=176) vs. 122007


title: Parental Liver Pool (n=176) vs. 109001


title: Parental Liver Pool (n=176) vs. 109015


title: Parental Liver Pool (n=176) vs. 109007


title: Parental Liver Pool (n=176) vs. 109004


title: Parental Liver Pool (n=176) vs. 109003


title: Parental Liver Pool (n=176) vs. 108021


title: Parental Liver Pool (n=176) vs. 108023


title: Parental Liver Pool (n=176) vs. 108022


title: Parental Liver Pool (n=176) vs. 108020


title: Parental Liver Pool (n=176) vs. 108018


title: Parental Liver Pool (n=176) vs. 108002


title: Parental Liver Pool (n=176) vs. 108006


title: Parental Liver Pool (n=176) vs. 108014


title: Parental Liver Pool (n=176) vs. 108013


title: Parental Liver Pool (n=176) vs. 108004


title: Parental Liver Pool (n=176) vs. 108015


title: Parental Liver Pool (n=176) vs. 107024


title: Parental Liver Pool (n=176) vs. 108008


title: Parental Liver Pool (n=176) vs. 108003


title: Parental Liver Pool (n=176) vs. 108012


title: Parental Liver Pool (n=176) vs. 108017


title: Parental Liver Pool (n=176) vs. 107020


title: Parental Liver Pool (n=176) vs. 107023


title: Parental Liver Pool (n=176) vs. 107021


title: Parental Liver Pool (n=176) vs. 107018


title: Parental Liver Pool (n=176) vs. 108010


title: Parental Liver Pool (n=176) vs. 108016


title: Parental Liver Pool (n=176) vs. 107019


title: Parental Liver Pool (n=176) vs. 107017


title: Parental Liver Pool (n=176) vs. 108011


title: Parental Liver Pool (n=176) vs. 107016


title: Parental Liver Pool (n=176) vs. 107014


title: Parental Liver Pool (n=176) vs. 107015


title: Parental Liver Pool (n=176) vs. 107005


title: Parental Liver Pool (n=176) vs. 107013


title: Parental Liver Pool (n=176) vs. 107012


title: Parental Liver Pool (n=176) vs. 107007


title: Parental Liver Pool (n=176) vs. 107002


title: Parental Liver Pool (n=176) vs. 107010


title: Parental Liver Pool (n=176) vs. 106024


title: Parental Liver Pool (n=176) vs. 107008


title: Parental Liver Pool (n=176) vs. 107009


title: Parental Liver Pool (n=176) vs. 106023


title: Parental Liver Pool (n=176) vs. 107001


title: Parental Liver Pool (n=176) vs. 106022


title: Parental Liver Pool (n=176) vs. 106021


title: Parental Liver Pool (n=176) vs. 107011


title: Parental Liver Pool (n=176) vs. 107006


title: Parental Liver Pool (n=176) vs. 106018


title: Parental Liver Pool (n=176) vs. 108024


title: Parental Liver Pool (n=176) vs. 106017


title: Parental Liver Pool (n=176) vs. 108019


title: Parental Liver Pool (n=176) vs. 106016


title: Parental Liver Pool (n=176) vs. 106012


title: Parental Liver Pool (n=176) vs. 106015


title: Parental Liver Pool (n=176) vs. 106013


title: Parental Liver Pool (n=176) vs. 106009


title: Parental Liver Pool (n=176) vs. 106007


title: Parental Liver Pool (n=176) vs. 106006


title: Parental Liver Pool (n=176) vs. 106011


title: Parental Liver Pool (n=176) vs. 106019


title: Parental Liver Pool (n=176) vs. 106010


title: Parental Liver Pool (n=176) vs. 106004


title: Parental Liver Pool (n=176) vs. 105018


title: Parental Liver Pool (n=176) vs. 106008


title: Parental Liver Pool (n=176) vs. 105023


title: Parental Liver Pool (n=176) vs. 105019


title: Parental Liver Pool (n=176) vs. 105024


title: Parental Liver Pool (n=176) vs. 106001


title: Parental Liver Pool (n=176) vs. 105022


title: Parental Liver Pool (n=176) vs. 105016


title: Parental Liver Pool (n=176) vs. 105020


title: Parental Liver Pool (n=176) vs. 105013


title: Parental Liver Pool (n=176) vs. 105012


title: Parental Liver Pool (n=176) vs. 105011


title: Parental Liver Pool (n=176) vs. 106003


title: Parental Liver Pool (n=176) vs. 105015


title: Parental Liver Pool (n=176) vs. 105010


title: Parental Liver Pool (n=176) vs. 105004


title: Parental Liver Pool (n=176) vs. 105008


title: Parental Liver Pool (n=176) vs. 105009


title: Parental Liver Pool (n=176) vs. 105001


title: Parental Liver Pool (n=176) vs. 105005


title: Parental Liver Pool (n=176) vs. 104024

value: BALB/cByJ


title: Parental Liver Pool (n=176) vs. 104023

value: Parental Liver Pool (n=176)


title: Parental Liver Pool (n=176) vs. 106014


title: Parental Liver Pool (n=176) vs. 105002


title: Parental Liver Pool (n=176) vs. 105014


title: Parental Liver Pool (n=176) vs. 104020


title: Parental Liver Pool (n=176) vs. 104022


title: Parental Liver Pool (n=176) vs. 104019


title: Parental Liver Pool (n=176) vs. 104017


title: Parental Liver Pool (n=176) vs. 104018


title: Parental Liver Pool (n=176) vs. 104015


title: Parental Liver Pool (n=176) vs. 104016


title: Parental Liver Pool (n=176) vs. 104013


title: Parental Liver Pool (n=176) vs. 104012


title: Parental Liver Pool (n=176) vs. 104011


title: Parental Liver Pool (n=176) vs. 104014


title: Parental Liver Pool (n=176) vs. 120023


title: Parental Liver Pool (n=176) vs. 120022


title: Parental Liver Pool (n=176) vs. 120016


title: Parental Liver Pool (n=176) vs. 104008


title: Parental Liver Pool (n=176) vs. 120015


title: Parental Liver Pool (n=176) vs. 104006


title: Parental Liver Pool (n=176) vs. 120011


title: Parental Liver Pool (n=176) vs. 120021


title: Parental Liver Pool (n=176) vs. 120009


title: Parental Liver Pool (n=176) vs. 105007


title: Parental Liver Pool (n=176) vs. 105021


title: Parental Liver Pool (n=176) vs. 104004


title: Parental Liver Pool (n=176) vs. 120017


title: Parental Liver Pool (n=176) vs. 120019


title: Parental Liver Pool (n=176) vs. 104002


title: Parental Liver Pool (n=176) vs. 104009


title: Parental Liver Pool (n=176) vs. 104003


title: Parental Liver Pool (n=176) vs. 120010


title: Parental Liver Pool (n=176) vs. 120014


title: Parental Liver Pool (n=176) vs. 104010


title: Parental Liver Pool (n=176) vs. 120012


title: Parental Liver Pool (n=176) vs. 120018


title: Parental Liver Pool (n=176) vs. 120006


title: Parental Liver Pool (n=176) vs. 120013


title: Parental Liver Pool (n=176) vs. 120007


title: Parental Liver Pool (n=176) vs. 120005


title: Parental Liver Pool (n=176) vs. 120004


title: Parental Liver Pool (n=176) vs. 120003


title: Parental Liver Pool (n=176) vs. 121020


title: Parental Liver Pool (n=176) vs. 120001


title: Parental Liver Pool (n=176) vs. 120002


title: Parental Liver Pool (n=176) vs. 121018


title: Parental Liver Pool (n=176) vs. 121023


title: Parental Liver Pool (n=176) vs. 121021


title: Parental Liver Pool (n=176) vs. 121013


title: Parental Liver Pool (n=176) vs. 121011


title: Parental Liver Pool (n=176) vs. 121007


title: Parental Liver Pool (n=176) vs. 121024


title: Parental Liver Pool (n=176) vs. 121014


title: Parental Liver Pool (n=176) vs. 121017


title: Parental Liver Pool (n=176) vs. 121008


title: Parental Liver Pool (n=176) vs. 121019


title: Parental Liver Pool (n=176) vs. 121009


title: Parental Liver Pool (n=176) vs. 121010


title: Parental Liver Pool (n=176) vs. 121002


title: Parental Liver Pool (n=176) vs. 103023

value: AKR/J


title: Parental Liver Pool (n=176) vs. 121004

value: M


title: Parental Liver Pool (n=176) vs. 121005


title: Parental Liver Pool (n=176) vs. 121001


title: Parental Liver Pool (n=176) vs. 103021


title: Parental Liver Pool (n=176) vs. 103020


title: Parental Liver Pool (n=176) vs. 103024


title: Parental Liver Pool (n=176) vs. 121003


title: Parental Liver Pool (n=176) vs. 103019


title: Parental Liver Pool (n=176) vs. 103018


title: Parental Liver Pool (n=176) vs. 103016


title: Parental Liver Pool (n=176) vs. 103015


title: Parental Liver Pool (n=176) vs. 103014


title: Parental Liver Pool (n=176) vs. 103013


title: Parental Liver Pool (n=176) vs. 103009


title: Parental Liver Pool (n=176) vs. 103008


title: Parental Liver Pool (n=176) vs. 102023

value: A/J


title: Parental Liver Pool (n=176) vs. 103005

value: F


title: Parental Liver Pool (n=176) vs. 103001


title: Parental Liver Pool (n=176) vs. 102022


title: Parental Liver Pool (n=176) vs. 102011


title: Parental Liver Pool (n=176) vs. 103006


title: Parental Liver Pool (n=176) vs. 102012


title: Parental Liver Pool (n=176) vs. 102019


title: Parental Liver Pool (n=176) vs. 102016


title: Parental Liver Pool (n=176) vs. 102018


title: Parental Liver Pool (n=176) vs. 103012


title: Parental Liver Pool (n=176) vs. 103017


title: Parental Liver Pool (n=176) vs. 102013


title: Parental Liver Pool (n=176) vs. 103004


title: Parental Liver Pool (n=176) vs. 103003


title: Parental Liver Pool (n=176) vs. 102021


title: Parental Liver Pool (n=176) vs. 102020


title: Parental Liver Pool (n=176) vs. 102014


title: Parental Liver Pool (n=176) vs. 102009


title: Parental Liver Pool (n=176) vs. 103002


title: Parental Liver Pool (n=176) vs. 102017


title: Parental Liver Pool (n=176) vs. 102010


title: Parental Liver Pool (n=176) vs. 102008


title: Parental Liver Pool (n=176) vs. 102007


title: Parental Liver Pool (n=176) vs. 102004


title: Parental Liver Pool (n=176) vs. 102005


title: Parental Liver Pool (n=176) vs. 102003


title: Parental Liver Pool (n=176) vs. 102002


title: Parental Liver Pool (n=176) vs. 102001


title: Parental Liver Pool (n=176) vs. 101008


title: Parental Liver Pool (n=176) vs. 101009


title: dcl1 seedlings, heat stress, 12h after treatment, replicate B

status: Public on May 08 2010

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: University of Oldenburg

description: Raw and normalized array data are provided as supplementary files per sample. Processed expression data are provided as additional supplementary files summarizing gene expression in M_001-M_012 as well pri-miRNA expression in M_001-M_012 as well as in S_014-S_026.

hyb_protocol: Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42°C. Arrays were washed using a Fluidics Station 450, wash protocol FS450_0001.

scan_protocol: Tiling arrays were scanned using a GeneChip® Scanner 3000 7G.

data_processing:
For identification of transcribed regions, data were background normalized, followed by quantile normalization and transcript normalization correction for probe sequence biases. For expression analysis of annotated genes, standard RMA normalization was applied (see Zeller et al., Plant J., 2009, and references therein for details)
Background-, quantile- and transcript-normalized values, log2 transformed (supplementary files for Series record)

label_protocol: 7.5 µg dsDNA was fragmented and labeled using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: For synthesis of targets, 1 µg of total RNA was used as template for generation of cRNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX, USA). We followed the manufacturer’s instruction with one exception: For tiling arrays, biotinylated NTPs were replaced by unmodified NTPs (stock solution 25 mM each).7 µg unmodified cRNA (for tiling arrays) was converted into dsDNA (GeneChip® WT Double-Stranded cDNA Synthesis Kit, Affymetrix, Santa Clara, CA, USA) and dsDNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany).

value: seedling

tag: treatment

value: 12h after transfer to liquid MS  at 30°C, LL, 0.5MS + 1% sucrose, 23°C, 7 days

tag: target

value: dsDNA, biotinylated

tag: replicate

value: B

tag: ecotype

value: Columbia

tag: genotype


title: dcl1 seedlings, cold stress, 12h after treatment, replicate B

value: 12h after transfer to liquid MS  at 10°C, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: dcl1 seedlings, heat stress, 1h after treatment, replicate A

value: 1h after transfer to liquid MS at 30°C, LL, 0.5MS + 1% sucrose, 23°C, 7 days

value: A


title: dcl1 seedlings, cold stress, 12h after treatment, replicate C

value: C


title: dcl1 seedlings, heat stress, 12h after treatment, replicate C


title: dcl1 seedlings, heat stress, 1h after treatment, replicate C


title: dcl1 seedlings, heat stress, 1h after treatment, replicate B


title: dcl1 seedlings, heat stress, 12h after treatment, replicate A


title: dcl1 seedlings, cold stress, 1h after treatment, replicate C

value: 1h after transfer to liquid MS at 10°C, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: dcl1 seedlings, cold stress, 12h after treatment, replicate A


title: dcl1 seedlings, cold stress, 1h after treatment, replicate B


title: Parental Liver Pool (n=176) vs. 101002


title: Parental Liver Pool (n=176) vs. 101007


title: Parental Liver Pool (n=176) vs. 101024


title: dcl1 seedlings, cold stress, 1h after treatment, replicate A


title: Parental Liver Pool (n=176) vs. 101018


title: Parental Liver Pool (n=176) vs. 101017


title: Parental Liver Pool (n=176) vs. 101023


title: Parental Liver Pool (n=176) vs. 101022


title: dcl1 seedlings, ABA treatment, 12h after treatment, replicate C

value: 12h after transfer to liquid MS  with 100µM ABA, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: dcl1 seedlings, ABA treatment, 1h after treatment, replicate C

value: 1h after transfer to liquid MS with 100µM ABA, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: dcl1 seedlings, ABA treatment, 12h after treatment, replicate B


title: Parental Liver Pool (n=176) vs. 101014

value: Parental Liver Pool (n=176)


title: Parental Liver Pool (n=176) vs. 101015


title: Parental Liver Pool (n=176) vs. 101011


title: dcl1 seedlings, osmotic stress, 12h after treatment, replicate B

value: 12h after transfer to liquid MS  with 300mM Mannitol, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: Parental Liver Pool (n=176) vs. 101004


title: Parental Liver Pool (n=176) vs. 101003


title: dcl1 seedlings, osmotic stress, 1h after treatment, replicate C

value: 1h after transfer to liquid MS with 300mM Mannitol, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: dcl1 seedlings, osmotic stress, 12h after treatment, replicate A


title: dcl1 seedlings, ABA treatment, 12h after treatment, replicate A


title: dcl1 seedlings, ABA treatment, 1h after treatment, replicate B


title: Parental Liver Pool (n=176) vs. 101013

value: M


title: Parental Liver Pool (n=176) vs. 101005

value: F


title: dcl1 seedlings, ABA treatment, 1h after treatment, replicate A

value: seedling


title: dcl1 seedlings, osmotic stress, 12h after treatment, replicate C


title: Parental Liver Pool (n=176) vs. 101006


title: Parental Liver Pool (n=176) vs. 101016


title: Parental Liver Pool (n=176) vs. 101012


title: Parental Liver Pool (n=176) vs. 101019


title: dcl1 seedlings, osmotic stress, 1h after treatment, replicate A


title: dcl1 seedlings, salt stress, 12h after treatment, replicate B

value: 12h after transfer to liquid MS  with 150mM NaCl, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: dcl1 seedlings, salt stress, 1h after treatment, replicate C

value: 1h after transfer to liquid MS with 150mM NaCl, LL, 0.5MS + 1% sucrose, 23°C, 7 days

value: dsDNA, biotinylated


title: Parental Liver Pool (n=176) vs. 101021


title: dcl1 seedlings, salt stress, 1h after treatment, replicate B

value: B

value: Columbia


title: dcl1 seedlings, salt stress, 1h after treatment, replicate A


title: dcl1 seedlings, salt stress, 12h after treatment, replicate A


title: dcl1 seedlings, mock control, 12h after treatment, replicate A

value: 12h after transfer to liquid MS, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: dcl1 seedlings, mock control, 1h after treatment, replicate B

value: 1h after transfer to liquid MS, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: dcl1 seedlings, mock control, 12h after treatment, replicate C

value: C


title: dcl1 seedlings before treatment, replicate C

value: 0.5MS + 1% sucrose, 23°C, 7 days, before transfer


title: dcl1 seedlings before treatment, replicate A

value: A


title: dcl1 seedlings, mock control, 12h after treatment, replicate B


title: dcl234 seedlings, replicate C

source_name: dcl234 seedlings, replicate C

value: Plants were grown for 7 days on half strength MS media at 23°C and LL.


title: dcl234 seedlings, replicate B

source_name: dcl234 seedlings, replicate B


title: dcl234 seedlings, replicate A

source_name: dcl234 seedlings, replicate A


title: rdr6 seedlings, replicate B

source_name: rdr6 seedlings, replicate B


title: rdr6 seedlings, replicate A

source_name: rdr6 seedlings, replicate A


title: se seedlings, replicate B

source_name: se seedlings, replicate B

value: se


title: se seedlings, replicate C

source_name: se seedlings, replicate C


title: rdr6 seedlings, replicate C

source_name: rdr6 seedlings, replicate C


title: dcl1 seedlings, salt stress, 12h after treatment, replicate C


title: dcl1 seedlings, mock control, 1h after treatment, replicate C


title: se seedlings, replicate A

source_name: se seedlings, replicate A


title: hyl1 seedlings, replicate A

source_name: hyl1 seedlings, replicate A


title: hyl1 seedlings, replicate B

source_name: hyl1 seedlings, replicate B


title: dcl1 seedlings before treatment, replicate B


title: dcl1 seedlings, replicate C

source_name: dcl1 seedlings, replicate C


title: dcl1 seedlings, replicate A

source_name: dcl1 seedlings, replicate A


title: WT seedlings, replicate C

source_name: WT seedlings, replicate C

value: WT


title: dcl1 seedlings, replicate B

source_name: dcl1 seedlings, replicate B


title: WT seedlings, replicate B

source_name: WT seedlings, replicate B


title: dcl234 inflorescences, replicate B

source_name: dcl234 inflorescences, replicate B

value: inflorescences

value: Plants were grown for 28 days on soil at 23°C and LL.


title: dcl234 inflorescences, replicate A

source_name: dcl234 inflorescences, replicate A


title: rdr6 inflorescences, replicate B

source_name: rdr6 inflorescences, replicate B


title: WT seedlings, replicate A

source_name: WT seedlings, replicate A


title: rdr6 inflorescences, replicate C

source_name: rdr6 inflorescences, replicate C


title: rdr6 inflorescences, replicate A

source_name: rdr6 inflorescences, replicate A


title: se inflorescences, replicate B

source_name: se inflorescences, replicate B


title: se inflorescences, replicate C

source_name: se inflorescences, replicate C


title: hyl1 inflorescences, replicate C

source_name: hyl1 inflorescences, replicate C


title: se inflorescences, replicate A

source_name: se inflorescences, replicate A


title: hyl1 seedlings, replicate C

source_name: hyl1 seedlings, replicate C


title: hyl1 inflorescences, replicate B

source_name: hyl1 inflorescences, replicate B


title: dcl1 inflorescences, replicate C

source_name: dcl1 inflorescences, replicate C

value: Plants were grown for more than 40 days on soil at 23°C and LL.


title: hyl1 inflorescences, replicate A

source_name: hyl1 inflorescences, replicate A


title: WT inflorescences, replicate C

source_name: WT inflorescences, replicate C


title: dcl1 inflorescences, replicate A

source_name: dcl1 inflorescences, replicate A


title: dcl1 inflorescences, replicate B

source_name: dcl1 inflorescences, replicate B


title: dcl1 seedlings, mock control, 1h after treatment, replicate A

value: seedling


title: WT inflorescences, replicate B

source_name: WT inflorescences, replicate B


title: dcl234 inflorescences, replicate C

source_name: dcl234 inflorescences, replicate C


title: WT inflorescences, replicate A

source_name: WT inflorescences, replicate A


title: Gcr2 deletion_3

status: Public on Mar 01 2010

city: Zurich

first: Sarah-Maria

last: Fendt

country: Switzerland

institute: ETH Zurich

description: deletion mutant

hyb_protocol: Biotin labeled cRNA samples  were fragmented randomly to 35-200 bp at 94°C in fragmentation buffer (Affymetrix Inc., P/N 900371) and  suspended in 100ml of hybridization mix (Affymetrix Inc., P/N 900720), containing a hybridization control and control oligonucleotide B2 (Affymetrix Inc., P/N 900454). Samples were hybridized to GeneChip Yeast Genome 2.0 arrays for16h at 45°C.

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

data_processing: Affymetrix CEL files were processed using  R (version 2.8.0) (R Development Core Team, 2008) and the Bioconductor affy package. Probe intensities were normalized for background by using the robust multiarray average method (RMA), using only perfect match (PM) probes. Normalization was performed using the qsplines algorithm. Gene expression values were calculated from the PM probes using the expression index calculation method (Li and Wong, 2001).

organism: Saccharomyces cerevisiae

source_name: Gcr2 deletion mutant

label_protocol: Total RNA samples  were reverse-transcribed with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using the Sample Cleanup Module (Affymetrix Inc.,P/N 900371). The purified double-stranded cDNAs were in vitro transcribed with biotin labeled nucleotides using the IVT Labeling Kit (Affymetrix Inc., P/N 900449).

growth_protocol: minimal medium, glucose as carbon source, 30°C, 300 rpm, exponential growth in batch

extract_protocol: extraction as explained in mechanical disruption protocol of the RNAesy Mini Kit (50), Quiagen

treatment_protocol: harvesting as explained in mechanical disruption protocol of the RNAesy Mini Kit (50), Quiagen

tag: genotype/variation

value: Gcr2 deletion


title: dcl1 seedlings, osmotic stress, 1h after treatment, replicate B

tag: tissue

value: 1h after transfer to liquid MS with 300mM Mannitol, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: Control 05-07

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description:
Gene expression data from human motor neurons
10 um cervical spinal cord frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.
From each individual 1000 motor neurons (MN) were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Mouse Genome 430A GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

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

source_name: Control 05-07

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol: PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

value: cervical spinal cord

tag: disease status

value: Neurologically normal control

tag: cell type

value: motor neuron


title: Control CC4

source_name: Control CC4


title: Control 85-07

source_name: Control 85-07


title: F344 at day40, biological rep2

status: Public on Feb 10 2010

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression interrogating 31099 transcripts

hyb_protocol: Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.

scan_protocol: After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.

data_processing: Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.

organism: Rattus norvegicus

source_name: Healthy control rats

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: Congenic BB rats, F344 rats and F344lyp rats  were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.

extract_protocol: Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)

treatment_protocol: When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.

value: pancreatic islets

value: healthy F344 strain

tag: age

value: 40 days old


title: wild-type FY4_2

description: wild-type

source_name: wild-type (FY4)

value: wildtype


title: JB at day40, biological rep1

source_name: Diabetes inducible rats, no mutation at LYP locus

value: JB strain (diabetes resistant, but inducible)


title: Gcr2 deletion_1

description: deletion mutant


title: F344 at day40, biological rep1


title: JB at day40, biological rep2


title: Control 39-97

source_name: Control 39-97


title: Control 12-07

source_name: Control 12-07


title: wild-type FY4_3

description: wild-type


title: Gcr2 deletion_2

description: deletion mutant


title: F344lyp at day40, biological rep1

value: healthy F344lyp strain


title: F344lyp at day40, biological rep2


title: PBS treated serum_DRlyp/lyprat_day40_rep2

status: Public on Dec 17 2009

hyb_protocol: Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit, and hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual.

scan_protocol: RNA from each culture was independently analyzed.  After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned using the GeneChip Scanner 3000.  Image data were quantified with Affymetrix Expression Console Software.

data_processing: The quantified raw signal intensites were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios.  Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated).  Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups.  Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/).  Hierarchical clustering was conducted with Genesis software.

source_name: DRlyp/lyp rats treated with PBS, rep2

growth_protocol: Brown Norway (BN) and BB rat colonies were maintained at the Medical College of Wisconsin, housed under specific pathogen-free conditions with standard light/dark cycles, and fed a regular diet and water ad libitum. All procedures were approved by the Medical College of Wisconsin Institutional Animal Care and Use Committee. Before sacrifice, animals were fasted for 16 hours, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer.  Animals possessing blood glucose levels above 250 mg/dl were disqualified from studies of pre-diabetes.  Animals were anesthetized under isofluorane during tissue collection.  Blood was collected by heart puncture (EDTA anti-coagulated) and plasma was immediately separated by centrifugation then stored at -80°C until use.

extract_protocol: Fresh PBMCs of healthy male Brown Norway (BN) donor rats (150-200 day old) were isolated from 5–8 ml of blood by Ficoll-Histopaque density gradient centrifugation and used immediately for cultures.  The induction of gene expression was accomplished by culturing the PBMCs of healthy day180 BN donor rats for 6 h at 37°C in 5% CO2 with a) 20% autologous BN plasma(10 replicates), b) allogeneic BN plasma (15 replicates), c) allogeneic DRlyp/lyp plasma (day 60, 4 replicates), or d) DR+/+ plasma (day 60, 4 replicates). Healthy BN PBMCs were also cultured with d60 DRlyp/lyp serum supplemented with IL-1RA (4 replicates) as well as autologous BN serum supplemented with IL-1B (4 replicates), to respectively block or induce IL-1 mediated gene expression. To determine if IL-1RA-treatment of DRlyp/lyp rats would result in modulation of the DRlyp/lyp signature, additional DRlyp/lyp rats were treated with hIL-1RA (n=6) or PBS (n=6). Rats were treated for 10 days, beginning at d30, then serum was collected at d40 and used to induce gene expression in PBMCs isolated from healthy d180 BN rats. Thus, there are a total of 53 chips being the addition of all the sample conditions mentioned above.

treatment_protocol: Human recombinant IL-1RA (Anakinra, Amgen) was delivered daily to animals by intraperitoneal (i.p.) injection in buffered saline at a dosage of 350 ug/kg/day.  Control littermates received an equal volume of saline.  After 45 days of age, blood glucose was measured 2-3 times per week, via tail venipuncture (5 μl).  Diabetes onset was defined as the first of two consecutive blood glucose measurements exceeding 250mg/dl.

tag: serum culture age

value: 40 days


title: PBS treated serum_DRlyp/lyprat_day40_rep4

source_name: DRlyp/lyp rats treated with PBS, rep4


title: Control 35-96

source_name: Control 35-96


title: PBS treated serum_DRlyp/lyprat_day40_rep6

source_name: DRlyp/lyp rats treated with PBS, rep6


title: JBlyp/lyp at day40, biological rep1

source_name: Diabetes prone rats, with homozygous mutation at LYP locus

value: Jblyp/lyp strain (diabetes prone)


title: PBS treated serum_DRlyp/lyprat_day40_rep3

source_name: DRlyp/lyp rats treated with PBS, rep3


title: Control CC2

source_name: Control CC2


title: PBS treated serum_DRlyp/lyprat_day40_rep5

source_name: DRlyp/lyp rats treated with PBS, rep5


title: wild-type FY4_1

description: wild-type


title: PBS treated serum_DRlyp/lyprat_day40_rep1

source_name: DRlyp/lyp rats treated with PBS, rep1


title: DR+/+ at day40, biological rep1

value: DR strain (diabetes resistant, but inducible)


title: JBlyp/lyp at day40, biological rep2


title: DR+/+ at day40, biological rep2


title: Autologous serum_BNrat_rep6

source_name: autologous BN serum, rep6

value: 180 days


title: Autologous serum_BNrat_rep1

source_name: autologous BN serum, rep1


title: Autologous serum_BNrat_rep10

source_name: autologous BN serum, rep10


title: Autologous serum_IL1B_BNrat_rep1

source_name: autologous BN serum supplemented with IL-1B, rep1


title: Allogeneic serum_Drlyp/lyp_day60_rep2

source_name: d60 DRlyp/lyp serum, rep2

value: 60 days


title: Autologous serum_IL1B_BNrat_rep3

source_name: autologous BN serum supplemented with IL-1B, rep3


title: Autologous serum_BNrat_rep4

source_name: autologous BN serum, rep4


title: Autologous serum_BNrat_rep8

source_name: autologous BN serum, rep8


title: Allogeneic serum_Drlyp/lyp_day60_rep4

source_name: d60 DRlyp/lyp serum, rep4


title: Autologous serum_BNrat_rep3

source_name: autologous BN serum, rep3


title: Autologous serum_IL1B_BNrat_rep2

source_name: autologous BN serum supplemented with IL-1B, rep2


title: Allogeneic serum_DR++rat_day60_rep1

source_name: d60 DR++ serum, rep1


title: Autologous serum_BNrat_rep5

source_name: autologous BN serum, rep5


title: Allogeneic serum_DR++rat_day60_rep3

source_name: d60 DR++ serum, rep3


title: Autologous serum_IL1B_BNrat_rep4

source_name: autologous BN serum supplemented with IL-1B, rep4


title: Allogeneic serum_BNrat_rep13

source_name: allogeneic BN serum, rep13


title: Autologous serum_BNrat_rep9

source_name: autologous BN serum, rep9


title: Autologous serum_BNrat_rep7

source_name: autologous BN serum, rep7


title: Autologous serum_BNrat_rep2

source_name: autologous BN serum, rep2


title: Allogeneic serum_DR++rat_day60_rep4

source_name: d60 DR++ serum, rep4


title: Allogeneic serum_Drlyp/lyp_day60_rep1

source_name: d60 DRlyp/lyp serum, rep1


title: Allogeneic serum_Drlyp/lyp_day60_rep3

source_name: d60 DRlyp/lyp serum, rep3


title: Allogeneic serum_BNrat_rep15

source_name: allogeneic BN serum, rep15


title: Allogeneic serum_BNrat_rep12

source_name: allogeneic BN serum, rep12


title: Allogeneic serum_DR++rat_day60_rep2

source_name: d60 DR++ serum, rep2


title: Allogeneic serum_BNrat_rep14

source_name: allogeneic BN serum, rep14


title: Allogeneic serum_BNrat_rep10

source_name: allogeneic BN serum, rep10


title: Allogeneic serum_BNrat_rep11

source_name: allogeneic BN serum, rep11


title: Allogeneic serum_BNrat_rep7

source_name: allogeneic BN serum, rep7


title: Allogeneic serum_BNrat_rep5

source_name: allogeneic BN serum, rep5


title: Allogeneic serum_BNrat_rep9

source_name: allogeneic BN serum, rep9


title: 4x At x 2x Aa hybird, biological rep3

status: Public on Oct 01 2009

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

description: compatible interspecies hybrid

hyb_protocol: Standard Affymetrix protocol for Tiling Array platform

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

data_processing: The data were analyzed with TAS (from Affymetrix) and TileMap software. Normalization was performed using the quantile normalization approach.

organism: Arabidopsis arenosa x Arabidopsis thaliana

source_name: compatible hybrid silques

label_protocol: Labeled cDNA was obtaine dusing the Affymetrix whole genome transcriptome protocol using 7 ug total RNA

growth_protocol: Plant grown in 16 h light and 8 h dark in growth chamber conditions.

extract_protocol: Qiagen total RNA extraction kit was used according to the manufacturer's instructions.

treatment_protocol: Flowers were emasculated and then pollinated with A. arenosa pollen next morning

tag: seed survival high

tag: 5 DAP


title: Allogeneic serum_IL1RA_DRlyp/lyp_day60_rep4

source_name: d60 DRlyp/lyp serum supplemented with IL-1RA, rep4


title: Replicate 1

status: Public on Oct 30 2009

first: Tom

last: Zahrt

address: 8701 Watertown Plank Rd

department: Microbiology and Molecular Genetics

description: Analysis used wild-type RNA as a control to compare against RNA obtained from pepD deletion strain

hyb_protocol: Hybridization buffer (5x SSC, 0.1% SDS, 50% formamide) was added, and samples were hybridized using a Tecan HS 400 Pro hybridization station.  Slides were pre-hybridized (1% BSA, 0.1% SDS, 4x SSC) for 45min. Slides were washed sequentially using 2x SSC 0.1% SDS, 1x SSC, 0.2x SSC, and 0.05x SSC.

scan_protocol: Images were scanned using a GenePix 2500 scanner.

data_processing: Scanned images were processed and normalized using Scanalyze software.  Data output was processed using MS Excel and SAM.

organism: Mycobacterium tuberculosis

source_name: wild-type

label_protocol: 8 ug of total RNA was primed with random decamers, then reverse transcribed for 2h at 50C using 400 U SuperScript III RTase (Invitrogen) in the presence of 10 mM each of dATP, dGTP, dTTP, 2 mM dCTP, and 1 mM Cy3/Cy5 dCTP.

growth_protocol: Cultures were grown in standard 7H9 broth media until a desired OD600 of 0.4-0.6 was reached.

extract_protocol: Total RNA was fixed by treating the samples with RNAlater,and later extracted using RNAbee (Tel-test Inc).  Samples underwent phenol/chloroform extraction and isopropanol precipitation.  For clean up, samples were DNAse treated and purified using an RNeasy Kit (Qiagen).

source_name: mutant

value: delta pepD


title: Allogeneic serum_IL1RA_DRlyp/lyp_day40_rep2

source_name: d40 DRlyp/lyp serum supplemented with hIL-1RA, rep2


title: Allogeneic serum_BNrat_rep4

source_name: allogeneic BN serum, rep4


title: Allogeneic serum_IL1RA_DRlyp/lyp_day60_rep2

source_name: d60 DRlyp/lyp serum supplemented with IL-1RA, rep2


title: Allogeneic serum_BNrat_rep2

source_name: allogeneic BN serum, rep2


title: Allogeneic serum_IL1RA_DRlyp/lyp_day40_rep4

source_name: d40 DRlyp/lyp serum supplemented with hIL-1RA, rep4


title: Replicate 2


title: Allogeneic serum_IL1RA_DRlyp/lyp_day60_rep3

source_name: d60 DRlyp/lyp serum supplemented with IL-1RA, rep3


title: Allogeneic serum_IL1RA_DRlyp/lyp_day40_rep3

source_name: d40 DRlyp/lyp serum supplemented with hIL-1RA, rep3


title: Allogeneic serum_BNrat_rep8

source_name: allogeneic BN serum, rep8


title: Allogeneic serum_IL1RA_DRlyp/lyp_day40_rep6

source_name: d40 DRlyp/lyp serum supplemented with hIL-1RA, rep6


title: Allogeneic serum_BNrat_rep3

source_name: allogeneic BN serum, rep3


title: Allogeneic serum_BNrat_rep6

source_name: allogeneic BN serum, rep6


title: Dye-Flip Replicate 2


title: Replicate 3


title: Allogeneic serum_IL1RA_DRlyp/lyp_day60_rep1

source_name: d60 DRlyp/lyp serum supplemented with IL-1RA, rep1


title: Dye-Flip Replicate 1


title: Allogeneic serum_BNrat_rep1

source_name: allogeneic BN serum, rep1


title: Allogeneic serum_IL1RA_DRlyp/lyp_day40_rep5

source_name: d40 DRlyp/lyp serum supplemented with hIL-1RA, rep5


title: Allogeneic serum_IL1RA_DRlyp/lyp_day40_rep1

source_name: d40 DRlyp/lyp serum supplemented with hIL-1RA, rep1


title: 4x At x 2x Aa hybird, biological rep2

description: compatible interspecies hybrid

source_name: compatible hybrid silques


title: 4x At x 2x Aa hybird, biological rep1

description: compatible interspecies hybrid


title: 2x At x 2x Aa hybird, biological rep3

description: incompatible interspecies hybrid seed

source_name: incompatible hybrid silques

tag: seed lethality


title: 2x At x 2x Aa hybird, biological rep1

description: incompatible interspecies hybrid seed