title: 1174 DN2L condition cell line

description: SNP and CNV data

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files and were processed by Partek Genomics Suite.
Genetic CN events from Affymetrix chips were reported based on CN values using Partek’s Genomic Segmentation algorithm.  Single nucleotide polymorphism (SNP) genotype data was generated through Affymetrix’s Genotyping Console then imported into Partek and compared against a 270 HapMap genotype sample dataset

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from primary tissue and cell lines using the Qiagen DNA Mini Kit after disruption with a Qiagen Tissue Lyser. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer

tag: tissue


title: CDC1551 extra vs intracellular in activated macrophages rep 1

status: Public on Jul 09 2010

type: RNA

city: Ithaca

first: David

last: Russell

state: NY

address: C5 171 Veterinary Medical Center

department: College of Veterinary Medicine

country: USA

institute: Cornell University

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87360.gif

hyb_protocol: not provided

scan_protocol: GenePix Results 3

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

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: Extracellular CDC1551 strain

label_protocol: not provided

extract_protocol:
Extraction method = Trizol RNA extraction
Type of amplification prior to labeling: T7 RNA polymerase

treatment_protocol: Time: 24hrs; Growth Condition: Extracellularly grown

tag: strain

value: Extracellular CDC1551 strain

source_name: CDC1551 strain in activated macrophages

growth_protocol: Growth Conditions; Growth Temperature = 37oC; Static or Shaking = Static; Media = Middlebrook 7H9 supplemented with oleic acid-albumin-glucose-catalase complex (OADC; Difco), Tween 80 and glycerol

treatment_protocol: Time: 24hrs; Growth Condition: Grown in activated murine macrophages

value: CDC1551 strain in activated macrophages


title: CDC1551 Ctrl vs clinical isolate 2199-99_Uganda rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87215.gif

source_name: CDC1551 reference strain

value: reference strain cdc1551

source_name: Clinical isolate 2191-99_Uganda

growth_protocol: Growth Conditions; Starting OD = 0.05; Elapsed Time = 7 days; OD at Harvest = 0.5 - 0.6; Growth Temperature = 37oC; Static or Shaking = Static; Growth Vessel Volume = 25 cm^2; Media = Middlebrook 7H9 supplemented with oleic acid-albumin-glucose-catalase complex (OADC; Difco), Tween 80 and glycerol

value: clinical isolate 2199-99_uganda


title: CDC1551 Ctrl vs clinical isolate 1934-03_Beijing rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87208.gif

source_name: Clinical isolate 1934-03_Beijing

value: clinical isolate 1934-03_beijing


title: CDC1551 Ctrl vs clinical isolate 947-01_EAI rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87234.gif

source_name: Clinical isolate 947-01_EAI

value: clinical isolate 947-01_eai


title: Clinical isolate 12954-03_Beijing extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87332.gif

source_name: Extracellular Clinical isolate 12954-03_Beijing

source_name: Clinical isolate 12954-03_Beijing in activated macrophages


title: Clinical isolate 10517-01_Afri2 extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87330.gif

source_name: Extracellular Clinical isolate 10517-01_Afri2

source_name: Clinical isolate 10517-01_Afri2 in activated macrophages


title: CDC1551 Ctrl vs clinical isolate 12954-03_Beijing rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87200.gif

source_name: Clinical isolate 12954-03_Beijing

value: clinical isolate 12954-03_beijing


title: CDC1551 extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87361.gif

extract_protocol: not provided


title: Clinical isolate 1500-03_Beijing extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87334.gif

source_name: Extracellular Clinical isolate 1500-03_Beijing

source_name: Clinical isolate 1500-03_Beijing in activated macrophages


title: Clinical isolate 2336-02_Haarlem extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87347.gif

source_name: Extracellular Clinical isolate 2336-02_Haarlem

source_name: Clinical isolate 2336-02_Haarlem in activated macrophages


title: Clinical isolate 9532-03_Haarlem extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87357.gif

source_name: Extracellular Clinical isolate 9532-03_Haarlem

source_name: Clinical isolate 9532-03_Haarlem in activated macrophages


title: Brahman adult tick rep 2

city: Brisbane

first: Manuel

middle: Rodriguez

last: Valle

state: QLD

address: 665 Fairfield road, Yeerongpilly

department: Emerging Technologies

country: Australia

institute: DEEDI

description:
17 days old (soon after the 2nd tick moult from nymph to adult stages) approximately 500 young adult female ticks were collected from the Brahman cattle
A total of six tick naïve cattle, three Brahman and three Holstein-Friesian female cattle were infested with 1.5 g (~30,000) N strain larvae [31] and were kept grazing at the University of Queensland’s Pinjarra Hills campus. On Day 2, approximately 20,000 larvae were placed into a 24 cm2 mesh bag and attached to the neck of each animal for approx. 5 hrs in order for the larvae to ‘sense’ host stimuli while also in the presence of other attached ticks.  These ‘frustrated’ larvae from both the Brahman (B-FL) and Holstein-Friesian (H-FL) were subsequently frozen in liquid nitrogen for total RNA extraction. An additional 20,000 unattached larvae (L - unfed) were processed to provide a control larvae group without host stimulus. At 17 days (soon after the 2nd tick moult from nymph to adult stages) approximately 500 young adult female ticks were collected from the Brahman and Holstein-Friesian cattle and frozen for total RNA extraction. The sampling regime was repeated to provide biological replicates of each sample to improve the statistical significance of the gene expression data (1 and 2 denote biological replicates). The experimental samples were: unattached/unfed larvae: L1, L2.  “Frustrated” larvae: B-FL1; B-FL2 and HFL1; HFL 2. Attached adult female ticks (~17 days):  – B-AT1, B-AT2 and H-AT1, H-AT2. (B=Brahman; H=Holstein-Friesian; FL=frustrated larvae; AT=adult tick)

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

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

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

organism: Rhipicephalus microplus

source_name: Rhipicephalus (Boophilus) microplus (N strain)

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

extract_protocol: Total RNA extraction  RNA was prepared from whole frustrated larvae, and adult ticks collected as described above. The ticks were first ground in liquid nitrogen using a sterile mortar and pestle. Total RNA was isolated using the TRIzol® reagent according to the manufacturer’s protocol (GibcoBRL, USA). Total RNA was also prepared by the same procedure from 20 000 unattached/unfed larvae (L1 and L2). The mRNA was purified from these samples using the Poly (A) PuristTM MAG Kit (AMBION, USA) as recommended by the manufacturer.  cDNA Synthesis  cDNA was prepared from the above mRNA samples using the SuperScriptTM Double-Stranded cDNA Synthesis Kit (Invitrogen, USA) as recommended by the manufacturer with the exception that after the second strand cDNA synthesis is terminated by the addition of 0.5 M EDTA and before the phenol: chloroform: isoamyl alcohol step, a RNase A treatment step was included as recommended in the NimbleGen cDNA protocol (NimbleGen, USA). After this RNase A treatment the Superscript double stranded cDNA Synthesis protocol was followed as described in the technical manual. cDNA median size was verified by 1% agarose electrophoresis in TAE 1X, and 2 microg of each cDNA sample were sent to NimbleGen Systems Inc. (Madison, WI, USA) for microarray hybridization using the R. microplus custom array (NimbleGen Custom Design name: 2006-05-22_B_microplus_50mer_exp).

tag: genotype

value: Wild-type

tag: phenotype

value: Tick Field strain not resistant to acaricide

tag: sample type

value: Brahman adult tick

tag: developmental stage

value: adult


title: CDC1551 Ctrl vs H37Rv rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87238.gif

source_name: Lab strain H37Rv

value: Lab strain H37Rv


title: Clinical isolate 1797-03_EAI extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87336.gif

source_name: Extracellular Clinical isolate 1797-03_EAI

source_name: Clinical isolate 1797-03_EAI in activated macrophages


title: Clinical isolate 4130-02_Haarlem extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87348.gif

source_name: Extracellular Clinical isolate 4130-02_Haarlem

source_name: Clinical isolate 4130-02_Haarlem in activated macrophages


title: CDC1551 Ctrl vs clinical isolate 1934-03_Beijing rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87210.gif

source_name: CDC1551 reference strain

source_name: Clinical isolate 1934-03_Beijing


title: Brahman frustrate larvae rep 2

description:
FrustrateLarvae into a mesh bag and attached to the neck of each Brahman bovine to sense host stimuli in the presence of other attached ticks
A total of six tick naïve cattle, three Brahman and three Holstein-Friesian female cattle were infested with 1.5 g (~30,000) N strain larvae [31] and were kept grazing at the University of Queensland’s Pinjarra Hills campus. On Day 2, approximately 20,000 larvae were placed into a 24 cm2 mesh bag and attached to the neck of each animal for approx. 5 hrs in order for the larvae to ‘sense’ host stimuli while also in the presence of other attached ticks.  These ‘frustrated’ larvae from both the Brahman (B-FL) and Holstein-Friesian (H-FL) were subsequently frozen in liquid nitrogen for total RNA extraction. An additional 20,000 unattached larvae (L - unfed) were processed to provide a control larvae group without host stimulus. At 17 days (soon after the 2nd tick moult from nymph to adult stages) approximately 500 young adult female ticks were collected from the Brahman and Holstein-Friesian cattle and frozen for total RNA extraction. The sampling regime was repeated to provide biological replicates of each sample to improve the statistical significance of the gene expression data (1 and 2 denote biological replicates). The experimental samples were: unattached/unfed larvae: L1, L2.  “Frustrated” larvae: B-FL1; B-FL2 and HFL1; HFL 2. Attached adult female ticks (~17 days):  – B-AT1, B-AT2 and H-AT1, H-AT2. (B=Brahman; H=Holstein-Friesian; FL=frustrated larvae; AT=adult tick)

value: Brahman frustrate larvae

value: larvae


title: CDC1551 Ctrl vs clinical isolate 4130-02_Haarlem rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87225.gif

source_name: Clinical isolate 4130-02_Haarlem

value: clinical isolate 4130-02_haarlem


title: CDC1551 Ctrl vs clinical isolate 1500-03_Beijing rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87202.gif

source_name: Clinical isolate 1500-03_Beijing

value: clinical isolate 1500-03_beijing


title: Holstein-Friesian frustrate larvae rep 1

description:
Frustrate Larvae into a mesh bag and attached to the neck of each Holstein-Friesian bovine to sense host stimuli in the presence of other attached ticks
A total of six tick naïve cattle, three Brahman and three Holstein-Friesian female cattle were infested with 1.5 g (~30,000) N strain larvae [31] and were kept grazing at the University of Queensland’s Pinjarra Hills campus. On Day 2, approximately 20,000 larvae were placed into a 24 cm2 mesh bag and attached to the neck of each animal for approx. 5 hrs in order for the larvae to ‘sense’ host stimuli while also in the presence of other attached ticks.  These ‘frustrated’ larvae from both the Brahman (B-FL) and Holstein-Friesian (H-FL) were subsequently frozen in liquid nitrogen for total RNA extraction. An additional 20,000 unattached larvae (L - unfed) were processed to provide a control larvae group without host stimulus. At 17 days (soon after the 2nd tick moult from nymph to adult stages) approximately 500 young adult female ticks were collected from the Brahman and Holstein-Friesian cattle and frozen for total RNA extraction. The sampling regime was repeated to provide biological replicates of each sample to improve the statistical significance of the gene expression data (1 and 2 denote biological replicates). The experimental samples were: unattached/unfed larvae: L1, L2.  “Frustrated” larvae: B-FL1; B-FL2 and HFL1; HFL 2. Attached adult female ticks (~17 days):  – B-AT1, B-AT2 and H-AT1, H-AT2. (B=Brahman; H=Holstein-Friesian; FL=frustrated larvae; AT=adult tick)

value: Holstein-Friesian frustrate larvae


title: Holstein-Friesian adult tick rep 2

description:
17 days old (soon after the 2nd tick moult from nymph to adult stages) approximately 500 young adult female ticks were collected from the Holstein-Friesian cattle
A total of six tick naïve cattle, three Brahman and three Holstein-Friesian female cattle were infested with 1.5 g (~30,000) N strain larvae [31] and were kept grazing at the University of Queensland’s Pinjarra Hills campus. On Day 2, approximately 20,000 larvae were placed into a 24 cm2 mesh bag and attached to the neck of each animal for approx. 5 hrs in order for the larvae to ‘sense’ host stimuli while also in the presence of other attached ticks.  These ‘frustrated’ larvae from both the Brahman (B-FL) and Holstein-Friesian (H-FL) were subsequently frozen in liquid nitrogen for total RNA extraction. An additional 20,000 unattached larvae (L - unfed) were processed to provide a control larvae group without host stimulus. At 17 days (soon after the 2nd tick moult from nymph to adult stages) approximately 500 young adult female ticks were collected from the Brahman and Holstein-Friesian cattle and frozen for total RNA extraction. The sampling regime was repeated to provide biological replicates of each sample to improve the statistical significance of the gene expression data (1 and 2 denote biological replicates). The experimental samples were: unattached/unfed larvae: L1, L2.  “Frustrated” larvae: B-FL1; B-FL2 and HFL1; HFL 2. Attached adult female ticks (~17 days):  – B-AT1, B-AT2 and H-AT1, H-AT2. (B=Brahman; H=Holstein-Friesian; FL=frustrated larvae; AT=adult tick)

value: Holstein-Friesian adult tick


title: Clinical isolate 10514-01_Afri2 extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87328.gif

source_name: Extracellular Clinical isolate 10514-01_Afri2

source_name: Clinical isolate 10514-01_Afri2 in activated macrophages


title: Holstein-Friesian frustrate larvae rep 2


title: 1174 primary xenograft tissue

type: genomic

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

description: SNP and CNV data

label: biotin

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cell lines were grown in DN2L conditions (DMEM-F12 supplemented with 20ng/ml epidermal growth (EGF; Invitrogen), 20ng/ml basic fibroblast growth factor (bFGF; Invitrogen), 1:50 B27 supplement (Invitrogen), 1:100 N2 supplement (Invitrogen), 10ng/ml leukemia inhibitory factor (LIF; Chemicon)

tag: cell line

value: brain


title: 1174 primary xenograft cell line in DN2L condition

description: SNP and CNV data


title: Brahman adult tick rep 1


title: Holstein-Friesian adult tick rep 1


title: CDC1551 Ctrl vs clinical isolate 2333-99_Uganda rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87217.gif

value: reference strain cdc1551

source_name: Clinical isolate 2333-99_Uganda

value: clinical isolate 2333-99_uganda


title: H0027407: C1 - Total BM

city: Pasadena

first: Aadel

last: Chaudhuri

state: CA

address: 1200 E California Blvd

institute: Caltech

description: miRNA profiling

hyb_protocol: Standard Agilent labeling protocol.

scan_protocol: Standard Agilent labeling protocol.

data_processing: Variance Stabilization Normalization (vsn) algorithm was used to normalize data.

organism: Mus musculus

source_name: total bone marrow

label_protocol: Standard Agilent labeling protocol.

extract_protocol: RNA was extracted using Qiagen miRNeasy kit.

value: total bone marrow


title: Clinical isolate 4130-02_Haarlem extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87349.gif

value: Extracellular Clinical isolate 4130-02_Haarlem

value: Clinical isolate 4130-02_Haarlem in activated macrophages


title: H0027408: C2 - LKS

description: miRNA profiling

source_name: LKS cells

tag: cell type

value: LKS hematopoietic progenitor cells (isolated from bone marrow)


title: Clinical isolate 2169-99_Uganda extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87272.gif

source_name: Extracellular Clinical isolate 2169-99_Uganda

source_name: Clinical isolate 2169-99_Uganda in resting macrophages

treatment_protocol: Time: 24hrs; Growth Condition: Grown in resting murine macrophages


title: 1174 Primary tumor tissue

description: SNP and CNV data

source_name: 1174 primary tissue

value: 1174 primary tissue


title: CDC1551 Ctrl vs clinical isolate 1934-03_Beijing rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87209.gif

value: clinical isolate 1934-03_beijing


title: CDC1551 Ctrl vs clinical isolate 10514-01_Afri2 rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87195.gif

source_name: Clinical isolate 10514-01_Afri2

value: clinical isolate 10514-01_afri2


title: Clinical isolate 1500-03_Beijing extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87335.gif

source_name: Extracellular Clinical isolate 1500-03_Beijing

source_name: Clinical isolate 1500-03_Beijing in activated macrophages


title: CDC1551 Ctrl vs clinical isolate 1500-03_Beijing rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87204.gif


title: Clinical isolate 5468-02_Afri2 extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87352.gif

source_name: Extracellular Clinical isolate 5468-02_Afri2

source_name: Clinical isolate 5468-02_Afri2 in activated macrophages


title: CDC1551 Ctrl vs clinical isolate 2199-99_Uganda rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87216.gif

source_name: CDC1551 reference strain

source_name: Clinical isolate 2191-99_Uganda

value: clinical isolate 2199-99_uganda


title: Larvae rep 2

description:
unattached larvae (L - unfed) processed to provide a control larvae group without host stimulus
A total of six tick naïve cattle, three Brahman and three Holstein-Friesian female cattle were infested with 1.5 g (~30,000) N strain larvae [31] and were kept grazing at the University of Queensland’s Pinjarra Hills campus. On Day 2, approximately 20,000 larvae were placed into a 24 cm2 mesh bag and attached to the neck of each animal for approx. 5 hrs in order for the larvae to ‘sense’ host stimuli while also in the presence of other attached ticks.  These ‘frustrated’ larvae from both the Brahman (B-FL) and Holstein-Friesian (H-FL) were subsequently frozen in liquid nitrogen for total RNA extraction. An additional 20,000 unattached larvae (L - unfed) were processed to provide a control larvae group without host stimulus. At 17 days (soon after the 2nd tick moult from nymph to adult stages) approximately 500 young adult female ticks were collected from the Brahman and Holstein-Friesian cattle and frozen for total RNA extraction. The sampling regime was repeated to provide biological replicates of each sample to improve the statistical significance of the gene expression data (1 and 2 denote biological replicates). The experimental samples were: unattached/unfed larvae: L1, L2.  “Frustrated” larvae: B-FL1; B-FL2 and HFL1; HFL 2. Attached adult female ticks (~17 days):  – B-AT1, B-AT2 and H-AT1, H-AT2. (B=Brahman; H=Holstein-Friesian; FL=frustrated larvae; AT=adult tick)

source_name: Rhipicephalus (Boophilus) microplus (N strain)

value: Wild-type

value: Tick Field strain not resistant to acaricide


title: Clinical isolate 4850-03_EAI extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87351.gif

source_name: Extracellular Clinical isolate 4850-03_EAI

source_name: Clinical isolate 4850-03_EAI in activated macrophages


title: 2-12_DMSO-treatment-mutant_Rep3_ATH1

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: Sterilized by treatment with bleach Growth chamber Agar Murashige and Skoog basal salt mixture

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

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

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system.

organism: Arabidopsis thaliana

label_protocol: Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling

growth_protocol: Arabidopsis were grown vertically on MS agar plates for 2 weeks

extract_protocol: Seedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.

value: arr10 arr12 mutations

value: seedlings

value: roots

tag: stock code

tag: treatment

value: DMSO


title: 2-11_DMSO-treatment-mutant_Rep2_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: CDC1551 Ctrl vs clinical isolate 4130-02_Haarlem rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87223.gif

source_name: Clinical isolate 4130-02_Haarlem

value: clinical isolate 4130-02_haarlem


title: CDC1551 Ctrl vs clinical isolate 1500-03_Beijing rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87203.gif

value: reference strain cdc1551

source_name: Clinical isolate 1500-03_Beijing

value: clinical isolate 1500-03_beijing


title: 2-10_DMSO-treatment-mutant_Rep1_ATH1


title: Larvae rep 1

value: larvae


title: Clinical isolate 4130-02_Haarlem extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87280.gif

source_name: Extracellular Clinical isolate 4130-02_Haarlem

source_name: Clinical isolate 4130-02_Haarlem in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 10514-01_Afri2 rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87194.gif


title: Brahman frustrate larvae rep 1

description:
FrustrateLarvae into a mesh bag and attached to the neck of each Brahman bovine to sense host stimuli in the presence of other attached ticks
A total of six tick naïve cattle, three Brahman and three Holstein-Friesian female cattle were infested with 1.5 g (~30,000) N strain larvae [31] and were kept grazing at the University of Queensland’s Pinjarra Hills campus. On Day 2, approximately 20,000 larvae were placed into a 24 cm2 mesh bag and attached to the neck of each animal for approx. 5 hrs in order for the larvae to ‘sense’ host stimuli while also in the presence of other attached ticks.  These ‘frustrated’ larvae from both the Brahman (B-FL) and Holstein-Friesian (H-FL) were subsequently frozen in liquid nitrogen for total RNA extraction. An additional 20,000 unattached larvae (L - unfed) were processed to provide a control larvae group without host stimulus. At 17 days (soon after the 2nd tick moult from nymph to adult stages) approximately 500 young adult female ticks were collected from the Brahman and Holstein-Friesian cattle and frozen for total RNA extraction. The sampling regime was repeated to provide biological replicates of each sample to improve the statistical significance of the gene expression data (1 and 2 denote biological replicates). The experimental samples were: unattached/unfed larvae: L1, L2.  “Frustrated” larvae: B-FL1; B-FL2 and HFL1; HFL 2. Attached adult female ticks (~17 days):  – B-AT1, B-AT2 and H-AT1, H-AT2. (B=Brahman; H=Holstein-Friesian; FL=frustrated larvae; AT=adult tick)


title: CDC1551 Ctrl vs clinical isolate 5468-02_Afri2 rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87229.gif

source_name: Clinical isolate 5468-02_Afri2

value: clinical isolate 5468-02_afri2


title: CDC1551 Ctrl vs clinical isolate 2169-99_Uganda rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87212.gif

source_name: Clinical isolate 2169-99_Uganda

value: clinical isolate 2169-99_uganda


title: 2-8_TZ-treatment-mutant_Rep2_ATH1

value: trans-zeatin


title: 2-9_TZ-treatment-mutant_Rep3_ATH1

data_processing:
Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system.

*** The CEL file for Sample GSM507136 is truncated. A complete CEL file was requested but not provided. ***


title: 2-7_TZ-treatment-mutant_Rep1_ATH1


title: H37Rv extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87290.gif

source_name: Extracellular Lab strain H37Rv

value: Extracellular Lab strain H37Rv

source_name: H37Rv in resting macrophages

value: H37Rv in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 4850-03_EAI rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87226.gif

source_name: Clinical isolate 4850-03_EAI

value: clinical isolate 4850-03_eai


title: Clinical isolate 2336-02_Haarlem extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87277.gif

source_name: Extracellular Clinical isolate 2336-02_Haarlem

source_name: Clinical isolate 2336-02_Haarlem in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 1797-03_EAI rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87206.gif

source_name: Clinical isolate 1797-03_EAI

value: clinical isolate 1797-03_eai


title: 2-6_DMSO-treatment-wildtype_Rep3_ATH1

source_name: Col-0, wildtype, DMSO

tag: ecotype

value: wildtype


title: CDC1551 Ctrl vs clinical isolate 2333-99_Uganda rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87219.gif

source_name: CDC1551 reference strain

source_name: Clinical isolate 2333-99_Uganda

value: clinical isolate 2333-99_uganda


title: Clinical isolate 2191-99_Uganda extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87274.gif

source_name: Extracellular Clinical isolate 2191-99_Uganda

source_name: Clinical isolate 2191-99_Uganda in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 10517-01_Afri2 rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87197.gif

source_name: Clinical isolate 10517-01_Afri2

value: clinical isolate 10517-01_afri2


title: Clinical isolate 1797-03_EAI extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87268.gif

source_name: Extracellular Clinical isolate 1797-03_EAI

source_name: Clinical isolate 1797-03_EAI in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 947-01_EAI rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87232.gif

source_name: Clinical isolate 947-01_EAI

value: clinical isolate 947-01_eai


title: 2-4_DMSO-treatment-wildtype_Rep1_ATH1

description: Sterilized by treatment with bleach Growth chamber Agar Murashige and Skoog basal salt mixture

value: seedlings

value: roots


title: 2-5_DMSO-treatment-wildtype_Rep2_ATH1

value: DMSO


title: Clinical isolate 947-01_EAI extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87285.gif

source_name: Extracellular Clinical isolate 947-01_EAI

source_name: Clinical isolate 947-01_EAI in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 2199-99_Uganda rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87214.gif

value: reference strain cdc1551

source_name: Clinical isolate 2191-99_Uganda

value: clinical isolate 2199-99_uganda


title: Clinical isolate 12954-03_Beijing extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87264.gif

source_name: Extracellular Clinical isolate 12954-03_Beijing

source_name: Clinical isolate 12954-03_Beijing in resting macrophages


title: 2-3_CK-treatment-wildtype_Rep3_ATH1

data_processing:
Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system.

*** The CEL file for Sample GSM507130 is truncated. A complete CEL file was requested but not provided. ***

source_name: Col-0, wildtype, TZ


title: 2-2_CK-treatment-wildtype_Rep2_ATH1


title: H37Rv extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87289.gif

source_name: Extracellular Lab strain H37Rv

source_name: H37Rv in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 12954-03_Beijing rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87199.gif

source_name: Clinical isolate 12954-03_Beijing

value: clinical isolate 12954-03_beijing


title: Clinical isolate 2333-99_Uganda extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87276.gif

source_name: Extracellular Clinical isolate 2333-99_Uganda

source_name: Clinical isolate 2333-99_Uganda in resting macrophages


title: 2-1_CK-treatment-wildtype_Rep1_ATH1


title: CDC1551 Ctrl vs clinical isolate 4850-03_EAI rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87227.gif

source_name: CDC1551 reference strain

source_name: Clinical isolate 4850-03_EAI


title: Clinical isolate 10517-01_Afri2 extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87261.gif

source_name: Extracellular Clinical isolate 10517-01_Afri2

source_name: Clinical isolate 10517-01_Afri2 in resting macrophages


title: Clinical isolate 1934-03_Beijing extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87270.gif

source_name: Extracellular Clinical isolate 1934-03_Beijing

source_name: Clinical isolate 1934-03_Beijing in resting macrophages


title: 1-11_mut-flowers_Rep2_ATH1

description: Seeds were sown in soil, incubated at 4°C for 4 days in the dark, and then placed in constant conditions. Seeds were surface sterilised 10 minutes with 50% bleach, 0.2% SDS and rinsed 5 times with sterile water before sowed. Growth Room Commercial soil Levington M2 professional growing medium from The Scotts company (UK) Ltd (Paper Mill lane, Bramford, Ipswich, Suffolk, IP8 4BZ) lug-3 flowers show characteristic class A floral homeotic gene mutation defects ; sepals are staminoid/carpeloid, second whorl petals are either staminoid or absent and third-whorl stamens are fewer in number. The fourth whorl gynoecium exhibits unfused carpels with valves forming hornlike protrusions at the apex. These defects in floral organ identity and floral organ number were previously explained to be caused by ectopic expression of AG mRNA. AG independent defects are displayed by LUG mutants, and include abnormal carpel and ovule development, reduced female and male fertility, and narrower leaves and floral organs, suggesting that LUG has a wider role in floral development and a function in vegetative development. Further defects in vegetative development include first leaves variable in size between individuals, in the majority of the cases being smaller than wild type, possibly as a result of a retarded seedling development. Mature rosette leaves generally have longer petioles than wild type leaves. Plants are shorter with increased shoot branching, and develop between 6-10 lateral inflorescences from the rosette, which result in the development of many more inflorescences than wild type plants.

source_name: lug-3 in Ler-0 background, flowers

growth_protocol: Plants were grown in Aratrays (Arasytem, Beta Tech) under constant conditions (20°C, constant 2400 lux globe lighting). Biological insecticide Intercept 70WG was added to the water used to moisten the soil before sowing. Seeds were sown in soil, incubated at 4°C for 4 days, and placed in constant conditions. Watering was performed with tap water every two days avoiding saturation of the soil.

extract_protocol: Total RNA was isolated from mature rosette leaves following the Rneasy Plant Mini Kit from Qiagen. Briefly fresh tissue (pool of 20 plants) was collected manually and weighed. Immediately placed in liquid nitrogen and grinded with a mortar and pestle until a fine powder was obtained. According to the initial weight powder was decanted in liquid nitrogen-cooled Rnase-free microcentrifuge tubes (100mg of initial material per tube, ex if initial material was 500mg then powder divided in 5 tubes and in label specified they were from the same extraction). 500 microlitres of buffer RLT previously adjusted with B-mercaptoethanol was added to the samples and the tubes were placed in a vortex, vortexing for 5 minutes vigorously (Vortex Genie-2, setting 9, Scientific Industries). The lysate was pipetted directly onto a QIAshredder spin column and centrifuged for 2 minutes at 16.1g (Eppendorf Centrigue 5415D). 0.5V of ethanol was added to the cleared lysate, mixed by pipetting, applied onto the Rneasy mini column and centrifuged for 30 s at 14.7g. The column was after washed with buffer RW1 twice (first with 700 microlitres and after with 350 microlitres) and the on-column Dnase digestion performed. Dnase I solution was prepared by mixing 10 microlitres of Dnase I (1500 Kunits in 550 microlitres of Rnase-free water) with 70 microlitres of buffer RDD. 80 microlitres of Dnase I solution per sample was added onto the Rneasy silica-gel membrane and digestion was allowed for 15 minutes at 20 Celsius degrees. After the incubation time, columns were washed with 350 microlitres of buffer RW1 and centrifuged for 30 s at 14.7g. Then columns were placed into a new collection tube and washed with 500 microlitres of RPE buffer and centrifuged as before (30s, 14.7g). A final wash with 500 microlitres of RPE was carried out and samples were centrifuged for 2 minutes, at 14.7g. The columns were then placed in a new collection tube and centrifuged at 16.1g for 1 minute. Next, columns were placed into new Rnase free-collection tubes and 50 microlitres of Rnase-free water pipetted directly onto the membrane and incubated for 10 minutes before elution. To elute, samples were centrifuged for 1 minute at 14.7g. Concentration of RNA as well as the Ratio A260/A280 was determined for each sample. All the samples with a ratio near 2.0 from the same liquid-nitrogen grinded step were pool in the same collection tube and the RNA was precipitated. For the precipitation procedure, 1/10 volume of NaAC and 2 volumes of ethanol 100% were added to the pooled sample mixed by vortex and incubated overnight at -20 Celsius degrees. Next day samples were centrifuged 10 minutes at 16.1g and the pellet was washed once with ethanol 70%, centrifuged for 10 minutes at 16.1g and air-dried. Dryed pellets were resuspended in 30 microliters of Rnase-free water and concentration and Ratio A260/A280 determined. Samples with high quality were selected for the experiment.

tag: background

value: lug-3 mutation

value: flowers


title: 1-12_mut-flowers_Rep3_ATH1


title: CDC1551 Ctrl vs clinical isolate 1797-03_EAI rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87207.gif

source_name: Clinical isolate 1797-03_EAI


title: Clinical isolate 2169-99_Uganda extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87271.gif

source_name: Extracellular Clinical isolate 2169-99_Uganda

source_name: Clinical isolate 2169-99_Uganda in resting macrophages


title: Clinical isolate 5468-02_Afri2 extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87284.gif

source_name: Extracellular Clinical isolate 5468-02_Afri2

source_name: Clinical isolate 5468-02_Afri2 in resting macrophages


title: 1-7_WT-flowers_Rep1_ATH1

description: Seeds were sown in soil, incubated at 4°C for 4 days in the dark, and then placed in constant conditions. Seeds were surface sterilised 10 minutes with 50% bleach, 0.2% SDS and rinsed 5 times with sterile water before sowed. Growth Room Commercial soil Levington M2 professional growing medium from The Scotts company (UK) Ltd (Paper Mill lane, Bramford, Ipswich, Suffolk, IP8 4BZ) Wild type plants from the Landsberg erecta ecotype (Ler-0) have blunt siliques, upright stems, and bunched flowers; short petioles, usually upright stems and a compact inflorescence.

source_name: Ler-0 background, WT, flowers


title: 1-6_mut-leaves_Rep3_ATH1

description: Seeds were sown in soil, incubated at 4°C for 4 days in the dark, and then placed in constant conditions. Seeds were surface sterilised 10 minutes with 50% bleach, 0.2% SDS and rinsed 5 times with sterile water before sowed. Growth Room Commercial soil Levington M2 professional growing medium from The Scotts company (UK) Ltd (Paper Mill lane, Bramford, Ipswich, Suffolk, IP8 4BZ) every two days with tap water lug-3 flowers show characteristic class A floral homeotic gene mutation defects ; sepals are staminoid/carpeloid, second whorl petals are either staminoid or absent and third-whorl stamens are fewer in number. The fourth whorl gynoecium exhibits unfused carpels with valves forming hornlike protrusions at the apex. These defects in floral organ identity and floral organ number were previously explained to be caused by ectopic expression of AG mRNA. AG independent defects are displayed by LUG mutants, and include abnormal carpel and ovule development, reduced female and male fertility, and narrower leaves and floral organs, suggesting that LUG has a wider role in floral development and a function in vegetative development. Further defects in vegetative development include first leaves variable in size between individuals, in the majority of the cases being smaller than wild type, possibly as a result of a retarded seedling development. Mature rosette leaves generally have longer petioles than wild type leaves. Plants are shorter with increased shoot branching, and develop between 6-10 lateral inflorescences from the rosette, which result in the development of many more inflorescences than wild type plants.

source_name: lug-3 in Ler-0 background, leaves

value: matured rosette leaves


title: CDC1551 Ctrl vs clinical isolate 2336-02_Haarlem rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87221.gif

source_name: Clinical isolate 2336-02_Haarlem

value: clinical isolate 2336-02_haarlem


title: 1-9_WT-flowers_Rep3_ATH1


title: Clinical isolate 1797-03_EAI extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87267.gif

source_name: Extracellular Clinical isolate 1797-03_EAI

source_name: Clinical isolate 1797-03_EAI in resting macrophages


title: 1-8_WT-flowers_Rep2_ATH1


title: Clinical isolate 10514-01_Afri2 extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87260.gif

source_name: Extracellular Clinical isolate 10514-01_Afri2

source_name: Clinical isolate 10514-01_Afri2 in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 10517-01_Afri2 rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87196.gif

source_name: CDC1551 reference strain

source_name: Clinical isolate 10517-01_Afri2


title: 1-10_mut-flowers_Rep1_ATH1


title: 1-5_mut-leaves_Rep2_ATH1

data_processing:
Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system.

*** The CEL file for Sample GSM507061 is truncated. A complete CEL file was requested but not provided. ***


title: CDC1551 Ctrl vs clinical isolate 10517-01_Afri2 rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87198.gif


title: Clinical isolate 10517-01_Afri2 extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87262.gif

source_name: Extracellular Clinical isolate 10517-01_Afri2

source_name: Clinical isolate 10517-01_Afri2 in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 5468-02_Afri2 rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87231.gif

source_name: Clinical isolate 5468-02_Afri2

value: clinical isolate 5468-02_afri2


title: Clinical isolate 1934-03_Beijing extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87269.gif

source_name: Extracellular Clinical isolate 1934-03_Beijing

source_name: Clinical isolate 1934-03_Beijing in resting macrophages


title: Clinical isolate 5468-02_Afri2 extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87283.gif

value: Extracellular Clinical isolate 5468-02_Afri2

value: Clinical isolate 5468-02_Afri2 in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 1797-03_EAI rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87205.gif

source_name: Clinical isolate 1797-03_EAI

value: clinical isolate 1797-03_eai


title: CDC1551 Ctrl vs clinical isolate 2169-99_Uganda rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87213.gif

source_name: Clinical isolate 2169-99_Uganda

value: clinical isolate 2169-99_uganda


title: Clinical isolate 1500-03_Beijing extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87265.gif

source_name: Extracellular Clinical isolate 1500-03_Beijing

source_name: Clinical isolate 1500-03_Beijing in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 9532-03_Haarlem rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87236.gif

source_name: Clinical isolate 9532-03_Haarlem

value: clinical isolate 9532-03_haarlem


title: Clinical isolate 9532-03_Haarlem extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87288.gif

source_name: Extracellular Clinical isolate 9532-03_Haarlem

source_name: Clinical isolate 9532-03_Haarlem in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 10514-01_Afri2 rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87193.gif

source_name: Clinical isolate 10514-01_Afri2

value: clinical isolate 10514-01_afri2


title: 1-3_WT-leaves_Rep3_ATH1

description: Seeds were sown in soil, incubated at 4°C for 4 days in the dark, and then placed in constant conditions Seeds were surface sterilised 10 minutes with 50% bleach, 0.2% SDS and rinsed 5 times with sterile water before sowed Growth Room Commercial soil Levington M2 professional growing medium from The Scotts company (UK) Ltd (Paper Mill lane, Bramford, Ipswich, Suffolk, IP8 4BZ) every two days with tap water Wild type plants from the Landsberg erecta ecotype (Ler-0) have blunt siliques, upright stems, and bunched flowers; short petioles, usually upright stems and a compact inflorescence

source_name: Ler-0 background, WT, leaves

value: wildtype


title: CDC1551 Ctrl vs clinical isolate 2169-99_Uganda rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87211.gif


title: Clinical isolate 4850-03_EAI extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87281.gif

source_name: Extracellular Clinical isolate 4850-03_EAI

source_name: Clinical isolate 4850-03_EAI in resting macrophages


title: Clinical isolate 947-01_EAI extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87286.gif

source_name: Extracellular Clinical isolate 947-01_EAI

source_name: Clinical isolate 947-01_EAI in resting macrophages


title: 1-1_WT-leaves_Rep1_ATH1

data_processing:
Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system.

*** The CEL file for Sample GSM507057 is truncated. A complete CEL file was requested but not provided. ***


title: 1-4_mut-leaves_Rep1_ATH1

description: Seeds were sown in soil, incubated at 4°C for 4 days in the dark, and then placed in constant conditions. Seeds were surface sterilised 10 minutes with 50% bleach, 0.2% SDS and rinsed 5 times with sterile water before sowed. Growth Room Commercial soil Levington M2 professional growing medium from The Scotts company (UK) Ltd (Paper Mill lane, Bramford, Ipswich, Suffolk, IP8 4BZ) every two days with tap water lug-3 flowers show characteristic class A floral homeotic gene mutation defects ; sepals are staminoid/carpeloid, second whorl petals are either staminoid or absent and third-whorl stamens are fewer in number. The fourth whorl gynoecium exhibits unfused carpels with valves forming hornlike protrusions at the apex. These defects in floral organ identity and floral organ number were previously explained to be caused by ectopic expression of AG mRNA. AG independent defects are displayed by LUG mutants, and include abnormal carpel and ovule development, reduced female and male fertility, and narrower leaves and floral organs, suggesting that LUG has a wider role in floral development and a function in vegetative development. Further defects in vegetative development include first leaves variable in size between individuals, in the majority of the cases being smaller than wild type, possibly as a result of a retarded seedling development. Mature rosette leaves generally have longer petioles than wild type leaves. Plants are shorter with increased shoot branching, and develop between 6-10 lateral inflorescences from the rosette, which result in the development of many more inflorescences than wild type plants.

source_name: lug-3 in Ler-0 background, leaves


title: Clinical isolate 12954-03_Beijing extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87263.gif

source_name: Extracellular Clinical isolate 12954-03_Beijing

source_name: Clinical isolate 12954-03_Beijing in resting macrophages


title: Clinical isolate 10514-01_Afri2 extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87259.gif

source_name: Extracellular Clinical isolate 10514-01_Afri2

source_name: Clinical isolate 10514-01_Afri2 in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 5468-02_Afri2 rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87230.gif

source_name: CDC1551 reference strain

source_name: Clinical isolate 5468-02_Afri2


title: Clinical isolate 4130-02_Haarlem extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87279.gif

source_name: Extracellular Clinical isolate 4130-02_Haarlem

source_name: Clinical isolate 4130-02_Haarlem in resting macrophages


title: 1-6_upf3_Rep1_ATH1

description: Before sowing, seeds were placed at 4°C for 3 days Arabidopsis seedlings were grown in growth chambers at 22°C supplied with continuous light. Before sowing, seeds were placed at 4°C for 3 days for stratification. Individual seeds were planted on pre-wetted pots of 2 sq inches containing a mixture of 3:1 compost and sand previously treated with the insecticide Intercept. Pots were placed in trays and covered with propagators, which were removed 8 days after seed germination. Seedlings were watered regularly until the tissue was collected for RNA extraction. Growth chamber Commercial soil 65 21

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

source_name: SALK_025175, upf3 mutant

extract_protocol: Qiagen RNAeasy kit protocol

value: upf3 mutation

tag: age

value: 17 days

value: whole plant


title: 1-2_WT-leaves_Rep2_ATH1


title: CDC1551 Ctrl vs clinical isolate 947-01_EAI rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87233.gif

value: reference strain cdc1551

source_name: Clinical isolate 947-01_EAI

value: clinical isolate 947-01_eai


title: CDC1551 Ctrl vs clinical isolate 4130-02_Haarlem rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87224.gif

source_name: Clinical isolate 4130-02_Haarlem

value: clinical isolate 4130-02_haarlem


title: CDC1551 extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87258.gif

source_name: Extracellular CDC1551 strain

value: Extracellular CDC1551 strain

source_name: CDC1551 strain in resting macrophages

value: CDC1551 strain in resting macrophages


title: 1-7_upf3_Rep2_ATH1


title: 1-5_upf1_Rep2_ATH1

source_name: SALK_112922, upf1 mutant

value: upf1 mutation


title: 1-3_wildtype_Rep3_ATH1

source_name: Col-0, wildtype


title: 1-4_upf1_Rep1_ATH1


title: 1-2_wildtype_Rep2_ATH1

data_processing:
Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system.

*** The CEL file for Sample GSM477814 is truncated. A complete CEL file was requested but not provided. ***


title: CDC1551 Ctrl vs H37Rv rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87239.gif

source_name: Lab strain H37Rv

value: Lab strain H37Rv


title: CDC1551 Ctrl vs clinical isolate 9532-03_Haarlem rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87237.gif

source_name: Clinical isolate 9532-03_Haarlem


title: CDC1551 Ctrl vs clinical isolate 9532-03_Haarlem rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87235.gif


title: CDC1551 Ctrl vs clinical isolate 12954-03_Beijing rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87201.gif

source_name: Clinical isolate 12954-03_Beijing

value: clinical isolate 12954-03_beijing


title: CDC1551 Ctrl vs clinical isolate 2336-02_Haarlem rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87222.gif

source_name: Clinical isolate 2336-02_Haarlem

value: clinical isolate 2336-02_haarlem


title: Clinical isolate 2191-99_Uganda extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87273.gif

source_name: Extracellular Clinical isolate 2191-99_Uganda

source_name: Clinical isolate 2191-99_Uganda in resting macrophages


title: CDC1551 extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87257.gif


title: Clinical isolate 9532-03_Haarlem extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87287.gif

source_name: Extracellular Clinical isolate 9532-03_Haarlem

source_name: Clinical isolate 9532-03_Haarlem in resting macrophages


title: Clinical isolate 2336-02_Haarlem extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87278.gif

source_name: Extracellular Clinical isolate 2336-02_Haarlem

source_name: Clinical isolate 2336-02_Haarlem in resting macrophages


title: CDC1551 Ctrl vs H37Rv rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87240.gif

source_name: CDC1551 reference strain


title: 1-1_wildtype_Rep1_ATH1


title: Clinical isolate 1500-03_Beijing extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87266.gif

source_name: Extracellular Clinical isolate 1500-03_Beijing

source_name: Clinical isolate 1500-03_Beijing in resting macrophages


title: Clinical isolate 2333-99_Uganda extra vs intracellular in resting macrophages rep 1

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87275.gif

source_name: Extracellular Clinical isolate 2333-99_Uganda

source_name: Clinical isolate 2333-99_Uganda in resting macrophages


title: Clinical isolate 4850-03_EAI extra vs intracellular in resting macrophages rep 2

description:
Simple annotation: Macrophage, Resting
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87282.gif

source_name: Extracellular Clinical isolate 4850-03_EAI

source_name: Clinical isolate 4850-03_EAI in resting macrophages


title: CDC1551 Ctrl vs clinical isolate 2336-02_Haarlem rep 1

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87220.gif


title: SC (time 1) Replicate 3

status: Public on Jul 08 2010

city: La Jolla

first: Dwight

last: Kuo

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description: dye swap replicate

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Arrays scanned using Genepix 4000A scanner and GenePix 6.0 software

data_processing: Background subtraction and LOESS, missing values replaced by KNNimpute algorithm. Data was subsequently quantile normalized

organism: Saccharomyces cerevisiae

source_name: BY4741 time 1

label_protocol: Labeling performed using GE Healthcare Cyscribe First strand cDNA synthesis kit

growth_protocol: Grow samples at OD600 0.05 to 0.2. Treat half of sample with drug. Take samples at 0, 1/3, 2/3, 1, 2 and 4 doubling times (both treated and untreated).

extract_protocol: total RNA was extracted using hot phenol chloroform method. mRNA was isolated using Poly(A) purist kit (AM1916), Pool in equal amounts untreated samples for each replicate

treatment_protocol: Add fluconazole (4ug/mL for Sc and Cg, 0.06125ug/mL for Kl) at time 0

tag: test

tag: doubling time

source_name: Reference Pool SC

tag: reference

value: Reference Pool SC


title: SC (time 1) Replicate 3 Dye Swap

description: dye swap replicate


title: SC (time 2) Replicate 1 Dye Swap

description: dye swap replicate

source_name: BY4741 time 2


title: SC (time 2) Replicate 1

description: dye swap replicate


title: SC (time 4) Replicate 3

description: dye swap replicate

source_name: BY4741 time 4


title: SC (time 4) Replicate 3 Dye Swap

description: dye swap replicate


title: SC (time 4) Replicate 1 Dye Swap

description: dye swap replicate


title: SC (time 4) Replicate 1

description: dye swap replicate


title: SC (time 2) Replicate 3 Dye Swap

description: dye swap replicate


title: SC (time 2) Replicate 3

description: dye swap replicate


title: SC (time 1) Replicate 1 Dye Swap

description: dye swap replicate


title: SC (time 4) Replicate 2 Dye Swap

description: dye swap replicate


title: SC (time 1) Replicate 2

description: dye swap replicate


title: SC (time 4) Replicate 2

description: dye swap replicate


title: SC (time 1) Replicate 1

description: dye swap replicate


title: SC (time 1) Replicate 2 Dye Swap

description: dye swap replicate


title: SC (time 2) Replicate 2

description: dye swap replicate


title: SC (time 2) Replicate 2 Dye Swap

description: dye swap replicate


title: SC (time 2/3) Replicate 3 Dye Swap

description: dye swap replicate


title: SC (time 2/3) Replicate 2

description: dye swap replicate


title: SC (time 2/3) Replicate 2 Dye Swap

description: dye swap replicate


title: SC (time 2/3) Replicate 3

description: dye swap replicate


title: SC (time 2/3) Replicate 1

description: dye swap replicate


title: SC (time 2/3) Replicate 1 Dye Swap

description: dye swap replicate


title: pool7vs6 + pool6vs7

city: Heidelberg

first: Stefan

middle: M

last: Pfister

address: INF 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

description: Comparison of pooled tumor RNA 1 vs. pooled tumor RNA 2. Transcriptome analysis.

hyb_protocol: Hybridization was carried out at 37 °C in UltraHyb buffer (Ambion) on a GeneTAC hybridization station (Genomic Solutions).

scan_protocol: Arrays were scanned at a 5µm resolution with an Axon 4000B scanner (Axon Instruments, Burlingame, USA) and images analyzed using GenePix Pro 6.0 software (Axon Instruments). Results files containing all relevant raw data were processed by use of ChipYard microarray analysis platform software (developed in-house), the statistical programming language R (http://www.r-project.org), and packages of the Bioconductor project (http://bioconductor.org; Ihaka and Gentleman, 1996).

data_processing: Spots not recognized by the image analysis software GenePix Pro 5.0 (Axon Instruments) were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002). To eliminate low quality data, the data points were ranked according to spot homogeneity, as assayed by the ratio of median to mean fluorescence intensity, the ratio of spot to local background intensity and the standard deviation of the log2 ratios between spot replicates. Those data points ranked among the lower 20% were removed from the data set. Genes that could not be quantified in more than 33% of all experiments of the experimental series after filtering were excluded as well. The given log2-ratios are integrated color-switch data.

label: Cy3, Cy5

source_name: 6q gain

label_protocol: aRNA produced by T7 amplification was reversely transcribed and subsequently labeled using Klenow fragment and Cy-dUTPs.

extract_protocol: RNA was extracted using the Trizol reagent (Invitrogen, Carlsbad, CA). RNA purification was performed as recommended by the manufacturer. The aqueous phase containing RNA was mixed 1:2 with ethanol, applied to RNeasy mini columns (Qiagen, Hilden, Germany), and eluted as recommended. Quality of medulloblastoma RNA was examined with a high-resolution electrophoresis system, the Agilent Bioanalyzer 2100 (Agilent Technologies). Quantification of total RNA was performed using a NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies).

value: pooled RNA from 5 medulloblastomas with gain of chromosome 6q

label: Cy5, Cy3

source_name: 6q balanced

value: pooled RNA from 5 medulloblastomas with balanced chromosome 6q


title: SC (time 1/3) Replicate 3 Dye Swap

description: dye swap replicate


title: CDC1551 Ctrl vs clinical isolate 4850-03_EAI rep 3

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87228.gif

source_name: Clinical isolate 4850-03_EAI

value: clinical isolate 4850-03_eai


title: SC (time 1/3) Replicate 3

description: dye swap replicate


title: IgG 6

city: Collegeville

first: Yuchen

last: Bai

state: PA

address: 500 Arcola Road, S2316

department: CIBB

institute: Pfizer

description: chip F

hyb_protocol: Control and AR ChIPs and subsequent genome tiling array hybridization were performed by Genpathway, Inc. (San Diego, CA).

data_processing: Arrays were scanned, and analyzed using Affymetrix Tiling Analysis Software (TAS), bed files map to hg18

source_name: AR ChIP DNA from primary human muscle cells treated with DMSO for 8 hours

growth_protocol: Primary human skeletal muscle myoblasts (Lonza) were grown and maintained in SkGM-2 media (Lonza) following the manufacturer’s recommendations. For TaqMan experiments, proliferating cells were grown in modified SkGM-2 media lacking dexamethasone and containing 5% charcoal-stripped fetal bovine serum. Cells were differentiated in DMEM-F12 supplemented with 2% horse serum (Lonza) following the manufacturer’s recommendations.

extract_protocol: Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer (cells). Lysates were sonicated and the DNA sheared to an average length of 300-500bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (20-30 mg) was then pre-cleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using an antibody against AR (sc-13062, Santa Cruz Biotechnology, Inc.) or rabbit IgG (I-5006, Sigma) as a control. After incubation at 4°C overnight, protein A agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: Primary human skeletal myoblasts were treated with 30nM dihydrotestosterone (DHT) or an equal volume of DMSO for 8 hours. Treated cells were then fixed with 1% formaldehyde for 15 minutes and quenched with 0.125 M glycine.

value: Primary Human Muscle Cells

tag: antibody

value: Rabbit IgG

tag: antibody manufacturer

value: Sigma

tag: antibody catalog #

tag: lot #

value: unknown

value: DMSO

source_name: Primary Human Muscle Cells

value: input DNA


title: DHT 6

description: chip F

scan_protocol: Arrays were scanned, and analyzed using Affymetrix Tiling Analysis Software (TAS)

source_name: AR ChIP DNA from primary human muscle cells treated with 30nM DHT for 8 hours

label_protocol: Control and AR ChIPs and subsequent genome tiling array hybridization were performed by Genpathway, Inc. (San Diego, CA).

value: AR antibody

value: Santa Cruz

value: DHT


title: SC (time 1/3) Replicate 2 Dye Swap

description: dye swap replicate


title: pool1vs3 + pool3vs1

source_name: 17q gain

value: pooled RNA from 10 medulloblastomas with gain of chromosome 17q

source_name: 17q balanced

value: pooled RNA from 10 medulloblastomas with balanced chromosome 17q


title: Vehicle 6

description: chip F


title: CG (time 4) Replicate 2

description: dye swap replicate

organism: Nakaseomyces glabratus

source_name: CBS138 time 4

label_protocol: Labeling performed using GE Healthcare Cyscribe First strand total RNA synthesis kit

source_name: Reference Pool CG

value: Reference Pool CG


title: CG (time 4) Replicate 3 Dye Swap

description: dye swap replicate


title: CG (time 4) Replicate 2 Dye Swap

description: dye swap replicate


title: SC (time 1/3) Replicate 2

description: dye swap replicate


title: SC (time 1/3) Replicate 1 Dye Swap

description: dye swap replicate


title: CG (time 4) Replicate 3

description: dye swap replicate


title: SC (time 1/3) Replicate 1

description: dye swap replicate


title: CG (time 4) Replicate 1 Dye Swap

description: dye swap replicate


title: 72 hr

city: Matsuoka

first: Kenzo

last: Uchida

state: Fukui

address: Shimoaizuki 23

department: Department of Orthopaedics and Rehabilitation Medicine

country: Japan

institute: Fukui University Faculty of Medical Sciences

description: Gene expression 72 hr after stress in E15 Sprague-Dawley rats spinal cord

hyb_protocol: Following fragmentation, 20 µg of cRNA were hybridized for 16 hours at 45°C on the GeneChip® Rat Genome 230 2.0 Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450, and scanned using GeneChip Scanner 3000 7G.

data_processing: Microarray data was initially processed using GeneChip Operating Software (GCOS, Affymetrix). Signal intensity was calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as the normalization method.

organism: Rattus norvegicus

source_name: 72 hr after mechanical stress

label_protocol: Biotinylated cRNA were synthesized using the IVT Labeling Kit (Affymetrix).

growth_protocol: The spinal cords of Sprague-Dawley rat embryos were dissected out at post-coital day 15 and stripped of the dorsal root ganglia and meninges.

extract_protocol: The cultured cells on each well at 0, 2, 6, 12, 24, 48 and 72 hours were disrupted in a lysis buffer containing β-mercaptoethanol and the total RNA from five animals was pooled at each time point, and further purified using RNeasy® Mini Kit (Qiagen, Valencia, CA) and treated with DNase I (TaKaRa Bio, Ohtsu, Japan)

treatment_protocol: Dissected tissues were rinsed with cold Ca2+ -and Mg2+-free Hanks balanced salt solution (HBSS) supplemented with 4 g/L glucose, and incubated at 37°C for 20 minutes with 0.03% (w/v) trypsin solution in HBSS under mild shaking.

tag: strain

value: Sprague-Dawley

tag: tissue

value: cultured spinal cord cells


title: 6 hr

description: Gene expression 6 hr after stress in E15 Sprague-Dawley rats spinal cord

source_name: 6 hr after mechanical stress


title: 12 hr

description: Gene expression 12 hr after stress in E15 Sprague-Dawley rats spinal cord

source_name: 12 hr after mechanical stress


title: MBF-2

city: Irvine

first: Osvaldo

last: Marinotti

address: University of California, Irvine

department: Molecular Biology & Biochemistry

institute: University of California, Irvine

description: Gene expression data from adult females after two blood meals within the same gonotrophic cycle

hyb_protocol: 10 µg of this fragmented target cRNA was hybridized at 45 °C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip® Plasmodium/Anopheles Genome Array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed on a GeneChip Scanner 3000. The results were quantified and analysed using GCOS software (version 1.1.1, Affymetrix, Inc.).

data_processing: The results were quantified and analysed using GCOS software (version 1.1.1, Affymetrix, Inc.) using default values (scaling, target signal intensity = 500; normalization, all probe sets; parameters, all set at default values).

organism: Anopheles gambiae

source_name: whole body

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly (A)+ mRNA present in the isolated total RNA (10 µg total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA, USA) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds-cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA). 15 µg of the resulting biotin-tagged cRNA were fragmented to strands of 35–200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

growth_protocol: Larvae were fed on finely powdered fish food (Tetramind, Tetra Werke, Germany) mixed 1:1 with yeast powder. Adults (males and females) were kept in cages with access ad libitum to raisins and water. For blood feeding, four days old adult female mosquitoes were fed on mice anaesthetized with a mixture of ketamine and xylazine. Males and females were kept together in the cage until the first blood meal. Blood-fed females were transferred to a separate cage and kept without males for the remaining duration of the experiment. The transferred females were offered a second blood meal at 48 hours after the first blood meal and blood fed females were again transferred to a separate cage. Three biological samples, each composed of five mosquitoes that ingested two blood meals  were  collected at 24 hours after the second blood meal, The RNA was immediately extracted and stored at -80°C.

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA, USA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD, USA) and purified further by passing it through an RNeasy spin column (Qiagen, Chatsworth, CA, USA). Eluted total RNAs were quantified and a portion of the recovered material adjusted to a final concentration of 1 µg/µl. All starting total RNA samples were quality-assessed prior to beginning target preparation/processing steps by resolving a small amount of each sample (typically 25–250 ng/well) on to a RNA Laboratory-On-A-Chip (Caliper Technologies, Mountain View, CA, USA) that was evaluated on an Agilent Bioanalyser 2100 (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Animals were maintained at 25°C, 75–85% relative humidity and a 18/6 h light/dark cycle.

tag: gender

value: female

value: pink-eye

tag: protocol

value: fed two blood meals within the same gonotrophic cycle


title: Rice Kitaake Leaf  rep1

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA (Irizarry et al., 2003) normalization and log transformation

organism: Oryza sativa

source_name: leaves

label_protocol: Standard Affymetrix Express Labeling kit protocol

growth_protocol: Rice plants were cultivated in greenhouse conditions for 6 weeks before harvesting of leaf tissue for RNA extraction

extract_protocol: TRIZOL RNA extraction followed by on-column DNAase1 treatment and QIAGEN column clean up using manufacturer protocol

value: leaves

tag: cultivar

value: Kitaake

value: 6 wk


title: MBF-1


title: 0 hr

description: Gene expression 0 hr after stress in E15 Sprague-Dawley rats spinal cord

source_name: o hr after mechanical stress


title: MBF-3


title: Melanoma cell line UKRV-Mel-16a

first: Andreas

last: Gast

state: BW

department: Division of Molecular Genetic Epidemiology

institute: Gernman Cancer Research Center

description: Cell line with BRAF V600E mutation

hyb_protocol: RNA was converted into double stranded cDNA and cRNA and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: Image analysis was performed with the Affymetrix GeneChip Operating Software (GCOS version 1.4, MAS5) and for pair-wise comparisons of expression profiles. SAM (significance analysis of micro-arrays) was used for statistically significant changes in expression. Marker analysis was performed using GeneCluster 2.0.

source_name: Melanoma cell line UKRV-Mel-16a, derived from metastatic tumor

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen). Concentrations of  RNA were measured by UV spectrophotometry and the integrity of total RNA isolated from cell lines was determined on the Bioanalyzer 2100 System

tag: cell type

value: melanoma cell line derived from metastatic tumor

tag: cell line

tag: genotype/variation

value: BRAF V600E mutation


title: Rice Kitaake Leaf  rep3


title: 24 hr

description: Gene expression 24 hr after stress in E15 Sprague-Dawley rats spinal cord

source_name: 24 hr after mechanical stress


title: CG (time 4) Replicate 1

description: dye swap replicate


title: Rice Kitaake Leaf  rep2


title: 2 hr

description: Gene expression 2 hr after stress in E15 Sprague-Dawley rats spinal cord

source_name: 2 hr after mechanical stress


title: Melanoma cell line UKRV-Mel-15d

description: Cell line with NRAS Q61R mutation

source_name: Melanoma cell line Ma-Mel-15d, derived from metastatic tumor

value: NRAS Q61R mutation


title: 48 hr

description: Gene expression 48 hr after stress in E15 Sprague-Dawley rats spinal cord

source_name: 48 hr after mechanical stress


title: Melanoma cell line UKRV-Mel-19a

description: Cell line with NRAS Q61R mutation

source_name: Melanoma cell line Ma-Mel-19a, derived from metastatic tumor


title: CG (time 2) Replicate 3 Dye Swap

description: dye swap replicate

source_name: CBS138 time 2


title: CG (time 2) Replicate 3

description: dye swap replicate


title: Melanoma cell line UKRV-Mel-04

description: Cell line without abberation in BRAF or NRAS or CDKN2A

source_name: Melanoma cell line Ma-Mel-04, derived from metastatic tumor

value: wild type BRAF, NRAS, and CDKN2A


title: Melanoma cell line UKRV-Mel-05

source_name: Melanoma cell line Ma-Mel-05, derived from metastatic tumor


title: CG (time 2) Replicate 2 Dye Swap

description: dye swap replicate


title: Melanoma cell line UKRV-Mel-11

source_name: Melanoma cell line Ma-Mel-11, derived from metastatic tumor


title: Melanoma cell line Ma-Mel-40

description: Cell line with homozygous deletion at the CDKN2A locus

source_name: Melanoma cell line Ma-Mel-40, derived from metastatic tumor

value: homozygous deletion at the CDKN2A locus


title: CG (time 2) Replicate 1 Dye Swap

description: dye swap replicate

source_name: Reference Pool CG


title: Melanoma cell line Ma-Mel-08b

source_name: Melanoma cell line Ma-Mel-08b, derived from metastatic tumor


title: Melanoma cell line Ma-Mel-28

description: Cell line with NRAS Q61R mutation

source_name: Melanoma cell line Ma-Mel-28, derived from metastatic tumor


title: Melanoma cell line Ma-Mel-57

description: Cell line with BRAF V600E mutation

source_name: Melanoma cell line Ma-Mel-57, derived from metastatic tumor


title: CG (time 2) Replicate 2

description: dye swap replicate


title: CG (time 2) Replicate 1

description: dye swap replicate


title: Melanoma cell line Ma-Mel-43

description: Cell line with NRAS Q61R mutation

source_name: Melanoma cell line Ma-Mel-43, derived from metastatic tumor


title: SUZ12_siHOTAIR_foreskin_HOX

city: Stanford

first: Miao-Chih

last: Tsai

address: 269 Campus Drive, CCSR 2140

institute: Stanford University

description: SUZ12 ChIP vs. input in siHOTAIR foreskin fibroblasts.

hyb_protocol: Standard NimbleGen hybridization kits and protocols were used. Hybridization was performed in the NimbleGen MAUI 12 bay machine.

scan_protocol: Arrays were scanned with Axon scanner at 5 um resolution according to standard NimbleGen protocols.

data_processing: Arrays were processed using NimbleGen's standard protocol for NimbleScan 2.4 ChIP data extraction. Log2 ChIP/input ratios were created from the two raw pair files.

source_name: siHOTAIR foreskin fibroblasts, SUZ12 input

label_protocol: Input DNA was labeled with Cy3 and ChIP DNA was labeled with Cy5 using the Standard NimbleGen ChIP labeling protocol (1 ug of amplified ChIP DNA, direct incorporation of Cy-labeled primers with Klenow extension).

growth_protocol: DMEM.

extract_protocol: ChIP was performed on 4x10^6 fibroblast cells with rabbit anti-H3K4me2 (ab7766, #56293, Abcam), rabbit anti-LSD1 (ab17721, #703277, Abcam) and rabbit anti-SUZ12 (ab12073, #7333337, Abcam) antibodies using the Farnham ChIP protocol. ChIP DNA and input DNA were reverse-crossed at 65C overnight, QIAquick column-purified, and amplified using the Sigma WGA2 kit for 1 round of amplification.

treatment_protocol: Human foreskin fibroblasts (ATCC CRL-2091) were transfected with siGFP or siHOTAIR for 72 hrs. The cells were harvested for ChIP.

value: ATCC CRL-2091

value: foreskin fibroblasts

tag: treatment

value: siHOTAIR

tag: sample type

value: input

source_name: siHOTAIR foreskin fibroblasts, SUZ12 ChIP

value: ChIP

tag: antibody vendor

value: Abcam

tag: antibody lot #


title: CG (time 1) Replicate 3 Dye Swap

description: dye swap replicate

tag: reference

value: Reference Pool CG

source_name: CBS138 time 1

tag: test

tag: doubling time


title: Melanoma cell line Ma-Mel-02

source_name: Melanoma cell line Ma-Mel-02, derived from metastatic tumor


title: SUZ12_siGFP_foreskin_HOX

description: SUZ12 ChIP vs. input in siGFP foreskin fibroblasts.

source_name: siGFP foreskin fibroblasts, SUZ12 input

value: siGFP

tag: antibody

source_name: siGFP foreskin fibroblasts, SUZ12 ChIP

tag: antibody catalog #


title: Melanoma cell line Ma-Mel-08a

source_name: Melanoma cell line Ma-Mel-08a, derived from metastatic tumor


title: LSD1_siHOTAIR_foreskin_1of2

description: LSD1 ChIP vs. input in siHOTAIR foreskin fibroblasts.

data_processing: Arrays were processed using NimbleGen's standard protocol for Nimblescan 2.4 ChIP data extraction. Log2 ChIP/input ratios were created from the two raw pair files.

source_name: siHOTAIR foreskin fibroblasts, LSD1 input

extract_protocol: ChIP was performed on 4x10^6 fibroblast cells with rabbit anti-SUZ12 (ab12073, #7333337, Abcam) and rabbit anti-LSD1 (ab17721, #703277, Abcam) antibodies using the Farnham ChIP protocol. ChIP DNA and input DNA were reverse-crossed at 65C overnight, QIAquick column-purified, and amplified using the Sigma WGA2 kit for 1 round of amplification.

source_name: siHOTAIR foreskin fibroblasts, LSD1 ChIP


title: LSD1_siGFP_foreskin_1of2

description: LSD1 ChIP vs. input in siGFP foreskin fibroblasts.

source_name: siGFP foreskin fibroblasts, LSD1 input

source_name: siGFP foreskin fibroblasts, LSD1 ChIP


title: CG (time 1) Replicate 3

description: dye swap replicate


title: LSD1_siGFP_foreskin_HOX


title: CG (time 1) Replicate 2

description: dye swap replicate


title: CG (time 1) Replicate 1 Dye Swap

description: dye swap replicate


title: LSD1_siHOTAIR_foreskin_HOX


title: CG (time 1) Replicate 2 Dye Swap

description: dye swap replicate


title: GC17

city: Bangalore

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

state: Karnataka

address: UnitI, Discoverer building, ITPL

country: India

institute: Institute of Bioinformatics

description: Biological replicate 14.

hyb_protocol: Fragmented Cy3-labeled cRNA (850ng) of the control sample were mixed with equal amounts of Cy5-labeled cRNA of the gastric tumor sample, and the mixtures were hybridized onto 44K whole human genome DNA microarrays (Agilent Technologies) for 17 hrs at 65°C with constant rotation (10 rpm). The arrays were washed according to manufacturer’s instructions.

scan_protocol: Scanned on Agilent scanner G2565AA.

data_processing: Agilent Feature Extraction Software (v 9.5) was used for feature extraction. The feature extraction files from all the samples were uploaded to GeneSpring GX v10.1 (Agilent). Following intensity-dependent normalization (Lowess), the data was subjected to statistical analysis.

source_name: Adjacent normal gastric mucosa

label_protocol: Low RNA input linear amplification kit from Agilent was used and labeling was done based on manufacturer's instructions. cRNA from normal tissues were labeled with Cy3 and cRNA from tumor tissues were labeled with Cy5.

growth_protocol: Surgically resected gastric adenocarcinoma samples and their paired disease-free marginal nonmalignant tissue were obtained from 14 patients with gastric adenocarcinoma.

extract_protocol: Total RNA isolation using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

value: gastric mucosa

tag: malignancy state

value: nonmalignant

source_name: Gastric adenocarcinoma tissue

value: gastric adenocarcinoma

value: malignant


title: GC10

description: Biological replicate 9.

tag: tissue


title: SUZ12_siHOTAIR_foreskin_1of2


title: GC15

description: Biological replicate 12.


title: GC09

description: Biological replicate 8.


title: GC11

description: Biological replicate 10.


title: H3K4me2_siHOTAIR_foreskin_HOX

description: H3K4me2 ChIP vs. input in siHOTAIR foreskin fibroblasts.

source_name: siHOTAIR foreskin fibroblasts, H3K4me2 input

source_name: siHOTAIR foreskin fibroblasts, H3K4me2 ChIP


title: SUZ12_siGFP_foreskin_1of2


title: Melanoma cell line Ma-Mel-51

description: Cell line with BRAF V600E mutation

source_name: Melanoma cell line Ma-Mel-51, derived from metastatic tumor

value: melanoma cell line derived from metastatic tumor


title: GC13

description: Biological replicate 11.


title: LSD1_siHOTAIR_foreskin_2of2


title: GC16

description: Biological replicate 13.


title: CG (time 1) Replicate 1

description: dye swap replicate

source_name: Reference Pool CG


title: CG (time 2/3) Replicate 3 Dye Swap

description: dye swap replicate

source_name: CBS138 time 2/3


title: CG (time 2/3) Replicate 3

description: dye swap replicate


title: H3K4me2_siGFP_foreskin_HOX

description: H3K4me2 ChIP vs. input in siGFP foreskin fibroblasts.

source_name: siGFP foreskin fibroblasts, H3K4me2 input

source_name: siGFP foreskin fibroblasts, H3K4me2 ChIP


title: SUZ12_siHOTAIR_foreskin_2of2

source_name: siHOTAIR foreskin fibroblasts, SUZ12 input

source_name: siHOTAIR foreskin fibroblasts, SUZ12 ChIP


title: GC05

description: Biological replicate 4.


title: SUZ12_siGFP_foreskin_2of2

source_name: siGFP foreskin fibroblasts, SUZ12 input

source_name: siGFP foreskin fibroblasts, SUZ12 ChIP


title: KL (time 4) Replicate 3 Dye Swap

description: dye swap replicate

organism: Kluyveromyces lactis

source_name: Reference Pool KL

value: Reference Pool KL

source_name: NRRL Y-1140 time 4

value: NRRL Y-1140


title: GC07

description: Biological replicate 6.


title: GC02

description: Biological replicate 2.


title: LSD1_siGFP_foreskin_2of2

source_name: siGFP foreskin fibroblasts, LSD1 input


title: KL (time 4) Replicate 3

description: dye swap replicate


title: KL (time 4) Replicate 2 Dye Swap

description: dye swap replicate


title: CG (time 2/3) Replicate 2

description: dye swap replicate


title: KL (time 2) Replicate 3 Dye Swap

description: dye swap replicate

source_name: NRRL Y-1140 time 2


title: GC06

description: Biological replicate 5.

source_name: Adjacent normal gastric mucosa


title: KL (time 4) Replicate 1 Dye Swap

description: dye swap replicate


title: CG (time 2/3) Replicate 1 Dye Swap

description: dye swap replicate


title: GC08

description: Biological replicate 7.

source_name: Gastric adenocarcinoma tissue


title: CG (time 2/3) Replicate 2 Dye Swap

description: dye swap replicate


title: CG (time 2/3) Replicate 1

description: dye swap replicate


title: KL (time 4) Replicate 2

description: dye swap replicate


title: KL (time 2) Replicate 1 Dye Swap

description: dye swap replicate


title: CG (time 1/3) Replicate 3 Dye Swap

description: dye swap replicate

source_name: CBS138 time 1/3


title: KL (time 2) Replicate 3

description: dye swap replicate


title: KL (time 2) Replicate 1

description: dye swap replicate


title: KL (time 2) Replicate 2 Dye Swap

description: dye swap replicate


title: KL (time 1) Replicate 3 Dye Swap

description: dye swap replicate

source_name: NRRL Y-1140 time 1


title: GC01

description: Biological replicate 1.


title: GC04

description: Biological replicate 3.


title: KL (time 1) Replicate 2 Dye Swap

description: dye swap replicate


title: KL (time 1) Replicate 3

description: dye swap replicate


title: KL (time 4) Replicate 1

description: dye swap replicate


title: CG (time 1/3) Replicate 2 Dye Swap

description: dye swap replicate


title: CG (time 1/3) Replicate 2

description: dye swap replicate


title: KL (time 1) Replicate 2

description: dye swap replicate


title: IgG 1

description: chip A

source_name: AR ChIP DNA from primary human muscle cells treated with DMSO for 8 hours

value: Primary Human Muscle Cells

value: Rabbit IgG

tag: antibody manufacturer

value: Sigma

tag: lot #

value: unknown

value: DMSO

source_name: Primary Human Muscle Cells

value: input DNA


title: KL (time 1) Replicate 1 Dye Swap

description: dye swap replicate


title: CG (time 1/3) Replicate 1 Dye Swap

description: dye swap replicate

source_name: Reference Pool CG


title: KL (time 1) Replicate 1

description: dye swap replicate


title: IgG 5

description: chip E


title: Vehicle 5

description: chip E

value: AR antibody

value: Santa Cruz


title: CG (time 1/3) Replicate 3

description: dye swap replicate

value: Reference Pool CG


title: KL (time 2/3) Replicate 3 Dye Swap

description: dye swap replicate

source_name: NRRL Y-1140 time 2/3


title: CG (time 1/3) Replicate 1

description: dye swap replicate


title: KL (time 2/3) Replicate 2

description: dye swap replicate


title: Vehicle 1

description: chip A


title: Vehicle 7

description: chip G


title: KL (time 2) Replicate 2

description: dye swap replicate


title: KL (time 2/3) Replicate 3

description: dye swap replicate


title: IgG 2

description: chip B


title: KL (time 2/3) Replicate 2 Dye Swap

description: dye swap replicate


title: IgG 7

description: chip G


title: DHT 5

description: chip E

source_name: AR ChIP DNA from primary human muscle cells treated with 30nM DHT for 8 hours

value: DHT


title: Vehicle 2

description: chip B


title: DHT 1

description: chip A


title: DHT 2

description: chip B


title: KL (time 1/3) Replicate 3 Dye Swap

description: dye swap replicate

source_name: NRRL Y-1140 time 1/3


title: DHT 7

description: chip G


title: KL (time 2/3) Replicate 1

description: dye swap replicate


title: KL (time 2/3) Replicate 1 Dye Swap

description: dye swap replicate


title: IgG 3

description: chip C


title: Vehicle 3

description: chip C


title: DHT 3

description: chip C


title: DHT 4

description: chip D


title: KL (time 1/3) Replicate 3

description: dye swap replicate


title: KL (time 1/3) Replicate 2

description: dye swap replicate


title: Vehicle 4

description: chip D


title: KL (time 1/3) Replicate 1 Dye Swap

description: dye swap replicate


title: KL (time 1/3) Replicate 2 Dye Swap

description: dye swap replicate


title: KL (time 1/3) Replicate 1

description: dye swap replicate


title: IgG 4

description: chip D


title: JNK LOF embryos, biological rep2

status: Public on Jul 07 2010

city: Nice

first: Raphaël

last: Rousset

address: Parc Valrose, Centre de Biochimie

department: Institut Biologie Valrose, iBV

country: France

institute: CNRS, INSERM, Université Côte d'Azur

description: Gene expression data from JNK loss-of-function embryos

hyb_protocol: Hybridization was realized at the Affymetrix Platform located at the Institut Curie, Paris.

scan_protocol: Scan was done at the Affymetrix Platform located at the Institut Curie, Paris.

data_processing: Bioinformatics analysis was performed using RMA (Robust Multi-array Average) and SAM (Significance Analysis Microarray) under R/Bioconductor.

organism: Drosophila melanogaster

source_name: hep mutant Drosophila embryos

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (performed at the Affymetrix Platform located at the Institut Curie, Paris).

growth_protocol: Two hour egg collections were incubated at 25°C during the time necessary to obtain 85 to 90% embryo sundergoing dorsal closure (~9 hrs). Because of a certain variability of development that we were not able to control, a fraction of each embryo was systematically tested by dpp in situ hybridization, and the collections that were not corresponding to the definite criterion (above 85% of stage 13-14 embryos) were eliminated.

extract_protocol: Total RNA was prepared with the Qiagen RNeasy mini kit for animal tissues according to the manufacturer's instructions.

treatment_protocol: Embryos were dechorionated with 50% bleach, frozen in nitrogen liquid and stored at -80C. Embryos were homogenized in RLT buffer (QIAGEN)/b-mercaptoethanol using a conventional rotor–stator homogenizer.

value: dechorionated embryo

tag: genotype

value: y w heprev75/y w hep1

tag: age

value: stage 13-14 embryos


title: JNK GOF embryos, biological rep2

description: Gene expression data from JNK gain-of-function embryos

source_name: Drosophila embryos expressing hepACT with 69B-GAL4


title: WT embryos, biological rep2

description: Gene expression data from WT embryos used as a reference

source_name: WT Drosophila embryos

value: w


title: JNK GOF embryos, biological rep3


title: JNK GOF embryos, biological rep1


title: JNK LOF embryos, biological rep1


title: WT embryos, biological rep3


title: WT embryos, biological rep1


title: White adipose tissue in Fsp27 knockout mice (rep2)

city: Beijing

first: Yinxin

last: Zhang

address: Room C131, School of Medicine, Tsinghua University

department: School of Life Sciences

country: China

institute: Tsinghua University

description: Hybridization and data collection were carried out by the Microarray facility at the Institute of Molecular and Cell Biology in Singapore.

hyb_protocol: Affymetrix EukGE-WS2v4 Hybridization

scan_protocol: HP Affymetrix Gene Array Scanner

data_processing: Affymetrix GeneChip Operating Software (GCOS) version 1.4

label: Biotin

source_name: gonadal WAT of five Fsp27 knockout mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: TRIzol reagent (Invitrogen, USA)

tag: strain

value: WAT

value: Fsp27 knockout

tag: gender

value: male

value: 3 month


title: JNK LOF embryos, biological rep3


title: KN3

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: Carm1 knockout 3

hyb_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome 430 2.0 arrays.

scan_protocol: Affymetrix Scanner/protocol

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

source_name: CRAM1 KN mice (lungs)

label_protocol: For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer's instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.

extract_protocol: Total RNA was isolated using the RNAeasy kit (QIAGEN) following the manufacturer's instructions.

tag: genotype/variation

value: CRAM1 knockout

tag: tissue type

value: lung, when pups are at embryo stage 18.5 days