title: Synch_3-CytoB-4hC

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (4 hours)


title: Synch_3-EtOH-16hC

status: Public on Dec 11 2009

type: RNA

city: Barcelona

first: Marc

last: Güell

address: C/ Dr.Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

hyb_protocol: Hybridization and Scanning (Axon GenePix 4000) has been carried out in the Genomic Core Facility of EMBL-Heidelberg.

data_processing: After background subtraction quantile (Boltad 2003) normalization was done using the bioconductor package marray (Yang 2005)

molecule: total RNA

organism: Mycoplasmoides pneumoniae M129

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (16 hours)

label_protocol: 9μg of total RNA were used so as to carry out the reverse transcription using SuperScriptTM Indirect cDNA Labeling System from Invitrogen. This kit was used according manufacturer indication but two modifications were introduced in the protocol. Reverse transcription was carried out at 37ºC instead of 46ºC and the set of random hexamers (2uL of 2.5ug/uL) was used instead of polyT 20mers.

growth_protocol: Bacterial Strains and culture conditions: Mycoplasma pneumoniae is grown in 150 cm2 tissue culture flasks with 50mL of modified Hayflick medium with the following composition. The basic medium consisted of 18.4g of PPLO broth, 29.8g of HEPES,10 g glucose, 5mL of 0.5% phenol red, and 35mL of 2N NaOH per liter. Horse serum and penicillin were included to a final concentration of 20% and 100 U/mL, respectively.

extract_protocol: After growth , surface-attached cells are washed once with phosphate-buffered saline (PBS; 0.15M NaCl, 10mM sodium phosphate, pH 7.4) and immediately lysed in the cultivation flask by adding RLT buffer from the QiagenTM RNeasy Plus Mini Kit (Cat. Num. 74134). This isolation method is used for RNA extraction as it removes most RNAs smaller than 200 bases, thus preventing the synthesis of cDNA from tRNA. For cell lysis, 2mL of RLT buffer in presence of 20μL β-mercaptoethanol was used per cultivation flask. The purification is done according the manufacturers protocol.

tag: Strain M129

tag: whole organism


title: Synch_3-CytoB-0hC

scan_protocol: Hybridization and Scanning (Axon GenePix 4000) has been carried out in the Genomic Core Facility of EMBL-Heidelberg.

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, and a time 0 sample was taken


title: Synch_3-EtOH-18hC

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (18 hours)


title: GC_4-2h

source_name: M129 cells were collected after 2h


title: Synch_3-CytoB-6hC

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (6 hours)


title: Synch_3-EtOH-10hC

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (10 hours)


title: Synch_3-CytoB-8hC

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (8 hours)


title: Synch_3-EtOH-6hC


title: Synch_3-CytoB-14hC

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (14 hours)


title: Synch_3-EtOH-8hC


title: Synch_3-EtOH-12hC

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (12 hours)


title: Synch_3-EtOH-14hC


title: Synch_3-EtOH-0hC


title: Synch_3-EtOH-2hC

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (2 hours)


title: Synch_3-CytoB-2hC


title: Synch_3-EtOH-4hC


title: GC_2,_3-LpH4

source_name: GC_3D growth curve changing the medium to rich medium at pH 6.5 after 24 hours in culture, and collecting cells after 3 days at pH 6.5


title: GC_2,_3-LpH3

source_name: GC_3D growth curve changing the medium to rich medium at pH 6.5 after 24 hours in culture, and collecting cells after 2 days at pH 6.5


title: GC_2,_3-LpH2

source_name: GC_3D growth curve changing the medium to rich medium at pH 6.5 after 24 hours in culture, and collecting cells after 1 day at pH 6.5


title: GC_2,_3-Lac4

source_name: GC_3C growth curve changing the medium to rich medium + 60mM sodium lactate after 24 hours in culture, and collecting cells after 3 days in NaLac


title: GC_2,_3-Ac4

source_name: GC_3B growth curve changing the medium to rich medium + 10mM sodium acetate after 24 hours in culture, and collecting cells after  3 days in NaAc.


title: GC_2,_3-Lac2

source_name: GC_3C growth curve changing the medium to rich medium + 60mM sodium lactate after 24 hours in culture, and collecting cells after 1 days in NaLac


title: Starv-starv0h

source_name: M129 cells were grown for 3 days in rich medium (time 0h), then washed and changed to medium without glucose, and starved cells were collected at 0h


title: GC_2,_3-Lac3

source_name: GC_3C growth curve changing the medium to rich medium + 60mM sodium lactate after 24 hours in culture, and collecting cells after 2 days in NaLac


title: GC_2,_3-Ac3

source_name: GC_3B growth curve changing the medium to rich medium + 10mM sodium acetate after 24 hours in culture, and collecting cells after  2 days in NaAc.


title: GC_2,_3-NaCl2

source_name: GC_3A growth curve changing the medium to rich medium + 60mM NaCl after 24 hours in culture, and collecting cells after 1 days in NaCl. Osmolarity control for lactate experiment (GC_3C).


title: GC_2,_3-NaCl4

source_name: GC_3A growth curve changing the medium to rich medium + 60mM NaCl after 24 hours in culture, and collecting cells after  3 days in NaCl. Osmolarity control for lactate experiment (GC_3C).


title: GC_2,_3-MM12

source_name: Cells grown in minimal medium (v12) for 3 days, n=2


title: Synch_2-CytoB-8hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (8 hours)


title: GC_2,_3-Fresh1

source_name: GC_2 growth curve changing the medium every 12 hours and collecting cells after 1days in culture. Time 1 serves as control (day 1) for GC_3


title: GC_2,_3-Fresh2

source_name: GC_2 growth curve changing the medium every 12 hours and collecting cells after 2 days in culture. Time 1 serves as control (day 1) for GC_3


title: Synch_2-CytoB-4hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (4 hours)


title: Synch_2-CytoB-6hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (6 hours)


title: GC_2,_3-MM12-2


title: Synch_2-CytoB-0hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, a control time 0 sample was taken


title: GC_2,_3-Fresh3

source_name: GC_2 growth curve changing the medium every 12 hours and collecting cells after 3 days in culture. Time 1 serves as control (day 1) for GC_3


title: Synch_2-EtOH-20hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (20 hours)


title: Synch_2-EtOH-22hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (24 hours)


title: GC_2,_3-Fresh4

source_name: GC_2 growth curve changing the medium every 12 hours and collecting cells after  4 days in culture. Time 1 serves as control (day 1) for GC_3


title: Synch_2-CytoB-2hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (2 hours)


title: GC_2,_3-NaCl3

source_name: GC_3A growth curve changing the medium to rich medium + 60mM NaCl after 24 hours in culture, and collecting cells after  2 days in NaCl. Osmolarity control for lactate experiment (GC_3C).


title: GC_2,_3-Ac2

source_name: GC_3B growth curve changing the medium to rich medium + 10mM sodium acetate after 24 hours in culture, and collecting cells after 1 day in NaAc.


title: Synch_2-EtOH-24hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (22 hours)


title: Synch_2-EtOH-16hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (16 hours)


title: Synch_2-EtOH-12hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (12 hours)


title: Synch_2-EtOH-14hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (14 hours)


title: Synch_2-EtOH-0hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (16 hours)


title: Synch_2-CytoB-24hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (14 hours)


title: Synch_2-EtOH-4hB


title: Synch_2-EtOH-6hB


title: Synch_2-CytoB-22hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (12 hours)


title: Synch_2-EtOH-10hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (10 hours)


title: Synch_2-CytoB-18hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (8 hours)


title: Synch_2-CytoB-10hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, and a time 0 sample was taken


title: Synch_1-CytoB-16hA


title: Synch_2-CytoB-16hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (6 hours)


title: Synch_1-CytoB-8hA


title: Synch_2-EtOH-2hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (18 hours)


title: Synch_1-CytoB-4hA

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (4 hours)


title: Synch_1-CytoB-12hA


title: Synch_1-EtOH-18hA

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle) in new medium, and after 24 hours, time points every 2 hours were taken (including time 0) after chasing with new medium


title: Synch_1-CytoB-2hA

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (2 hours)


title: Synch_1-EtOH-14hA


title: Synch_1-CytoB-14hA


title: Synch_1-CytoB-6hA


title: Synch_1-CytoB-18hA


title: Synch_2-CytoB-20hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, Ethanol) in new medium, and after 24 hours, time points every 2 hours were taken  after chasing with new medium (10 hours)


title: Synch_1-EtOH-10hA


title: Synch_1-EtOH-12hA


title: Synch_1-EtOH-8hA


title: Synch_2-CytoB-12hB


title: Synch_1-CytoB-10hA


title: Synch_2-CytoB-14hB


title: Synch_1-CytoB-0hA


title: Synch_1-EtOH-16hA


title: Synch_1-EtOH-2hA


title: HS.60min.37C.60min

source_name: Before Lysis were incubated for 60 min at 43ºC and then put back to 37C for 60min


title: rif12

source_name: Cells were treated with ryfampycin(11ug/mL) 18hours


title: Synch_1-EtOH-0hA


title: rif7

source_name: Cells were treated with ryfampycin(11ug/mL)


title: rif8


title: HS.60min

source_name: Before Lysis were incubated for 60 min at 43ºC


title: rif11


title: rif9


title: HS.15min

source_name: Before Lysis were incubated for 15 min at 43ºC


title: rif5


title: rif10


title: Synch_2-EtOH-18hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (18 hours)


title: Synch_1-EtOH-6hA


title: Osmostress._5

source_name: Before Lysis the cells were in contact with 0.5M NaCl for 20 min.


title: rif4


title: non_adherent_2

source_name: B170 cells were grown in rich medium with constant shaking and samples were taken after  4, days in culture.

tag: Strain B170


title: non_adherent_1

source_name: B170 cells were grown in rich medium with constant shaking and samples were taken after 4, days in culture.


title: rif6


title: Mild.Oxidative.Stress._5

source_name: Before lysis the cells were in contact with 0.1% of Hydrogen peroxide for 25 min at 37ºC


title: Gentamycin_4

source_name: 80 ug/mL of Gentamycin were added 1 hour before lysis.


title: Fresh.Media._1

source_name: Before lysis were set the cells were in contact with fresh media


title: HS.30min

source_name: Before Lysis were incubated for 30 min at 43ºC


title: Starvation._4

source_name: Before Lysis the cells were in contact with 0% of Glucose for 1h.


title: Osmostress._4


title: Norfloxacin._4

source_name: Before lysis the cells were in contact with Norfloxacin 10 ug/mL


title: rif3


title: rif1


title: rif2


title: Synch_2-EtOH-8hB

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle, ethanol), and after 24 hours, time points were taken every 2 hours after chasing with fresh medium (8 hours)


title: Mitomycin.C._4

source_name: Before lysis the cells were in contact with Mitomycin C 5ug/mL


title: Synch_1-EtOH-4hA

source_name: M129 cells grown for 3 days in dishes, 50 ug/ml cytochalasin B was added (or vehicle) in new medium, and after 24 hours, time points every 2 hours were taken (including time 0) after chasing with new medium


title: M.Ox.St..15min_2

source_name: Before lysis the cells were in contact with 0.1% of Hydrogen peroxide for 15 min at 37ºC


title: M.Ox.St..10min_1

source_name: Before lysis the cells were in contact with 0.1% of Hydrogen peroxide for 10 min at 37ºC


title: M.Ox.St..5min_2

source_name: Before lysis the cells were in contact with 0.1% of Hydrogen peroxide for 5 min at 37ºC


title: M.Ox.St..15min_3


title: M.Ox.St..10min_3


title: X32ºC._3

source_name: RNA was purified after 144h growing at 32C


title: X37.2ºC._3

source_name: Rna is collected after 96h growth


title: X32ºC._1


title: X32ºC._2


title: M.Ox.St..5min_3


title: M.Ox.St..5min_1


title: X37ºC._3


title: M.Ox.St..15min_1

source_name: Before lysis the cells were in contact with 0.1% of Hydrogen peroxide for 55 min at 37ºC


title: Glycerol._3

source_name: Medium was supplemented with 1% glycerol during the growth. RNA was purified after 96h.


title: Sacarose._3

source_name: Glucose was replaced by the same concentration of sucrose in the medium. RNA was purified after 96h.


title: Starvation._3


title: Mannose._3

source_name: Glucose was replaced by the same concentration of manose in the medium. RNA was purified after 96h.


title: M.Ox.St..10min_2


title: Mitomycin.C._3


title: Fresh.media._3


title: X37.3C


title: Norfloxacin._3


title: Mild.Oxidative.Stress._3

source_name: Before lysis the cells were in contact with 0.1% of Hydrogen peroxide for 25 min at 37ºC


title: Severe.Oxidative.Stress._3

source_name: Before lysis the cells were in contact with 0.5% of Hydrogen peroxide for 25 min at 37ºC


title: Gentamycin._3

source_name: 80 ug/mL of Gentamycin were added 1 hour before lysis.


title: Fresh.media._2

source_name: Before lysis were set the cells were in contact with fresh media


title: GC_72h

hyb_protocol: Labeling, hybridization, staining and scanning is carried out in the EMBL Genomics Core Facility following Affymetrix recommendations

data_processing: CEL files are parsed together with BPMAP (probe basic annotation) file using AffxParser library implemented in R. Probes complete annotation is carried out using R scripting. NCBI ftp (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Mycoplasma_pneumoniae)is used as source for probe annotation.

label: biotin

source_name: RNA was collected after 72h growth

label_protocol: 9μg of total RNA are mixed with 4.5 μg  of random hexamers and incubated at 70C for 10min, then transferred on ice. The synthesis included 10μL of SuperScript II Reverse Transcriptase(20 U/μL, Invitrogen, P/N 18064-071), 20 μL of DTT(Invitrogen, P/N 18064-071) 100mM, 40 μL of 5x1st strand buffer(Invitrogen, P/N 18064-071), 5μL of 10mM dNTPs+dUTPs(Affymetrix, P/N 900813) and 2.4 μL of Actinomycin D(0.5mg/mL, Sigma, P/N A1410-5MG) in a total volume of 200 μL at 42C for 1h. Samples then are subjected to RNase treatment of 20min at 37C(30 U Rnase H, Affymetrix, P/N 900813, 60 U Rnase cocktail, Ambion). First-strand cDNA was column purified and fragmented. Fragmentation mixture was composed by 4.8 μL 10x cDNA fragmentation buffer(Affymetrix, P/N 900813), 5.5 μg of cDNA, 1μL APE(1000 U/μL, Affymetrix, P/N 900813), 1 μL UDG (10 U/μ/L, Affymetrix, P/N 900813) in 50 μL at 37C for 60 min. Fragmentation enzymes were inactivated at 93C for 2min.

growth_protocol: Bacterial Strains and culture conditions: Mycoplasma pneumoniae is grown in 75cm2 tissue culture flasks with 50mL of modified Hayflick medium with the following composition. The basic medium consisted of 18.4g of PPLO broth, 29.8g of HEPES,10 g glucose, 5mL of 0.5% phenol red, and 35mL of 2N NaOH per liter. Horse serum and penicillin were included to a final concentration of 20% and 100 U/mL, respectively.

extract_protocol: After growth , surface-attached cells are washed once with phosphate-buffered saline (PBS; 0.15M NaCl, 10mM sodium phosphate, pH 7.4) and immediately lysed in the cultivation flask by adding Quiazol lysis reagent from QiagenTM miRNeasy Kit (Cat. Num. 79674). This isolation method is used for RNA extraction and preserves most small of RNAs. For cell lysis, 1.5mL of Quiazol lysis reagent is used per cultivation flask. The purification is done according the manufacturers protocol.

tag: total RNA(including sRNAs)


title: GC_96h

scan_protocol: Labeling, hybridization, staining and scanning is carried out in the EMBL Genomics Core Facility following Affymetrix recommendations

source_name: RNA was collected after 96h growth


title: Heat.Shock._3

source_name: Before Lysis were incubated for 20 min at 43ºC


title: Mild.Oxidative.Stress._6


title: Sacarose._2


title: Gentamycin._2

source_name: 80 ug/mL of Gentamycin was added 1 hour before lysis.


title: Mannose._2


title: GC_2h

source_name: RNA was collected after 2h growth


title: GC_24h

source_name: RNA was collected after 24h growth


title: GC_48h

source_name: RNA was collected after 48h growth


title: GC_120h

source_name: RNA was collected after 120h growth


title: GC_12h

source_name: RNA was collected after 12h growth


title: Mitomycin.C._2

source_name: Before lysis the cells were in contact with 5ug/mL Mitomycin C


title: GC_144h

source_name: RNA was collected after 144h growth


title: Norfloxacin._2

source_name: Before lysis the cells were in contact with 10 ug/mL Norfloxacin


title: Cyt6

source_name: After 48h growth at 37C, Cells where treated 24h with 50ug/mL Cythocalasin B, RNA was collected after 20h


title: EtOH7

source_name: After 48h growth at 37C, Cells where treated 24h with the vector(1mL EtOH), RNA was collected after 24h


title: Cyt3

source_name: After 48h growth at 37C, Cells where treated 24h with 50ug/mL Cythocalasin B, RNA was collected after 8h


title: Cyt2

source_name: After 48h growth at 37C, Cells where treated 24h with 50ug/mL Cythocalasin B, RNA was collected after 4h


title: Cyt1

source_name: After 48h growth at 37C, Cells where treated 24h with 50ug/mL Cythocalasin B, RNA was collected after 0h


title: Cyt5

source_name: After 48h growth at 37C, Cells where treated 24h with 50ug/mL Cythocalasin B, RNA was collected after 16h


title: Cyt7

source_name: After 48h growth at 37C, Cells where treated 24h with 50ug/mL Cythocalasin B, RNA was collected after 24h


title: Mild.Oxidative.Stress._2

source_name: Before lysis the cells were in contact with 0.1% of Hydrogen peroxide for 25 min at 37ºC


title: Osmostress._2

source_name: Before Lysis the cells were in contact with 0.5M NaCl for 20 min.


title: Heat.Shock._2

source_name: Before Lysis were incubated for 20 min at 43ºC


title: EtOH5

source_name: After 48h growth at 37C, Cells where treated 24h with the vector(1mL EtOH), RNA was collected after 16h


title: Starvation._2

source_name: Before Lysis the cells were incubate in medium without glucose for 1h.


title: EtOH6

source_name: After 48h growth at 37C, Cells where treated 24h with the vector(1mL EtOH), RNA was collected after 20h


title: EtOH3

source_name: After 48h growth at 37C, Cells where treated 24h with the vector(1mL EtOH), RNA was collected after 8h


title: EtOH4

source_name: After 48h growth at 37C, Cells where treated 24h with the vector(1mL EtOH), RNA was collected after 12h


title: Glycerol._2

source_name: Medium was supplemented with 1% glycerol during the growth. RNA was purified after 96h.


title: Cyt4

source_name: After 48h growth at 37C, Cells where treated 24h with 50ug/mL Cythocalasin B, RNA was collected after 12h


title: Heat.Shock6


title: X37ºC

source_name: Rna is collected after 96h growth


title: Severe.Oxidative.Stress._2

source_name: Before lysis the cells were in contact with 0.5% of Hydrogen peroxide for 25 min at 37ºC


title: EtOH2

source_name: After 48h growth at 37C, Cells where treated 24h with the vector(1mL EtOH), RNA was collected after 4h


title: X37.2ºC._2


title: Glycerol


title: Fresh.media._4

source_name: Before lysis were set the cells were in contact with fresh media


title: MMC_45min

source_name: After 96h growth at 37C, RNA was collected after 45min Mitomycin C treatment(5ug/mL)


title: Mannose._1

source_name: Glucose was replaced by the same concentration of manose in the medium. RNA was purified after 96h.


title: MMC_30min

source_name: After 96h growth at 37C, RNA was collected after 30min Mitomycin C treatment(5ug/mL)


title: EtOH1

source_name: After 48h growth at 37C, Cells where treated 24h with the vector(EtOH 0.4%), RNA was collected after 0h


title: MMC_60min

source_name: After 96h growth at 37C, RNA was collected after 60min Mitomycin C treatment(5ug/mL)


title: MMC_15min

source_name: After 96h growth at 37C, RNA was collected after 15min Mitomycin C treatment(5ug/mL)


title: Sacarose

source_name: Glucose was replaced by the same concentration of sucrose in the medium. RNA was purified after 96h.


title: MMC_20min

source_name: After 96h growth at 37C, RNA was collected after 20min Mitomycin C treatment(5ug/mL)


title: Starvation

source_name: Before Lysis the cells were in contact with medium without glucose for 1h.


title: MMC_11min

source_name: After 96h growth at 37C, RNA was collected after 11min Mitomycin C treatment(5ug/mL)


title: Norfloxacin

source_name: Before lysis the cells were in contact with 10 ug/mL Norfloxacin


title: Mitomycin.C

source_name: Before lysis the cells were in contact with  5ug/mL Mitomycin C


title: MMC_8min

source_name: After 96h growth at 37C, RNA was collected after 8min Mitomycin C treatment(5ug/mL)


title: MMC_5min

source_name: After 96h growth at 37C, RNA was collected after min Mitomycin C treatment(5ug/mL)


title: MMC_0min

source_name: RNA was collected after 96h growth


title: MMC_2min

source_name: After 96h growth at 37C, RNA was collected after 2min Mitomycin C treatment(5ug/mL)


title: Heat.Shock

source_name: Before Lysis cells were incubated for 20 min at 43ºC


title: Severe.Oxidative.Stress

source_name: Before lysis the cells were in contact with 0.5% of Hydrogen peroxide for 25 min at 37ºC


title: Osmostress

source_name: Before Lysis the cells were in contact with 0.5M NaCl for 20 min.


title: Gentamycin

source_name: 80 ug/mL of Gentamycin were added 1 hour before lysis.


title: Mild.Oxidative.Stress._1

source_name: Before lysis the cells were in contact with 0.1% of Hydrogen peroxide for 25 min at 37ºC


title: X37.2ºC

source_name: Rna is collected after 96h growth


title: 37C_42C45min_37C40min

source_name: After 96h growth at 37C, 45min at 42 C, RNA was collected after 40 min again at 37C


title: 37C_42C45min_37C15min

source_name: After 96h growth at 37C, 45min at 42 C, RNA was collected after 15 min again at 37C


title: 37C_42C30min

source_name: After 96h growth at 37C, RNA was collected after 30 min HS induction(42C)


title: 37C_42C45min_37C30min

source_name: After 96h growth at 37C, 45min at 42 C, RNA was collected after 30 min again at 37C


title: ADULT_BRAIN_EC_MICROVASCULATURE_REPLICATE_1

status: Public on Dec 10 2009

city: Stockholm

first: Liqun

last: He

address: Scheelesvag 2

country: Sweden

institute: Karolinska Institute

hyb_protocol: Hybridization    Print post-processing:    Bake slides for 4 hours at 80°C OR UV-crosslink at 3000 joule.      Pre-hybridization:    Pre-hybridize slides for 1 hour prior hybridization in DIG Easy Hyb + 1% BSA at 42°C.  After pre-hybridization, the slides are washed briefly but thoroughly with water and dried by blowing with air.  Slides should be used the same day for hybridization    Hybridization:    1. add 2x15µl water to Array-It hybridization cassettes and add the 35-40µl hybridization buffer under the lifter cover slips.  2. hybridize for 1,5h at 44°C in a water bath. After 1,5h the temperature is lowered to 40°C and the hybridization continues over night.      Slide washing:    1. 5min in 2xSSC, 0.1%SDS  2. 5min in 1xSSC  3. 5min in 0.1xSSC  4. dry by blowing with air  5. scan    Shopping list, hybridization    • DIG Easy Hyb  Roche. Cat. No.: 1 603 558

scan_protocol: Scanning and raw data acquisition  Scanner: GenePix 4000B (Axon Instruments Inc.)  Scanner software: GenePix Pro 4.0 (Axon Instruments Inc.)  Feature extraction software: ImaGene 5.1 (BioDiscovery Inc.)    1. Turn on the scanner at least 15 minutes before start. Turn on the computer after the scanner.    2. Insert the slide, array side facing down and the text/barcode pointing towards you.    3. Open “Hardware Settings” and set the laser power to 100% in both channels.    4. Preview scan at low resolution (40um) to locate the array.    5. Select the scan area according to the preview scan.    6. Open “Hardware Settings” and set resolution to 5 um (pixel size = 5 um)    7. Scan a smaller area of the array and use the histogram tab to balance PMTs.   Approximate PMT gains ratio near 1. If A. Thaliana RNA spikes were added to both labeling reactions, the features containing A. Thaliana targets should be yellow (PMT ratio = 1) and close to saturation.  Make sure that the dynamic range is big and the background signal is low. Often the naked eye is good enough to determine if the background level is acceptable, but if the majority of signals are around 2000, the background is too high.    8. Scan one grid at a time.    9. Save both images as single tiff files    10. Upload tiff images representing the signals from the Cy3- and Cy5 channel from one grid in ImaGene    11. Align images using the auto alignment tool    12. Put a grid on top of the aligned images to select the areas where signal intensities shall be quantified    13.  Assign gene identifiers to every spot (Probe ID)    14. Quantify signal intensities and acquire data using default settings    15. Export results as text files (one per channel per grid) to use for normalization

data_processing: LOWESS normalized for individual grid, data obtained from log2 of processed Cy3/Cy5 signal. Bioconductor limma package was used for the data processing(2.9.11).

molecule: cytoplasmic RNA

organism: Mus musculus

source_name: ABEC (ADULT BRAIN EC (MICROVASCULATURE))

label_protocol: Amplification and Cy-dye labeling  cDNA production  Start with 200ng to 1µg of total RNA    TUBE 1  mix:  RNA in 8µl water  1µg (in 1µl) oligo dT T7 primer  mix by pipetting up and down and incubate at 70ºC for 10min, then leave the mixture at 42ºC.    TUBE 2  mix: 4µl first strand buffer   2µl DTT   2µl dNTP ultrapure   1µl RNasin   1µl template switch oligo (1µg/µl)  mix by pipetting up and down and incubate at 42ºC for 2min.    mix tube1 and tube2 by pipetting up and down and incubate immediately at 42ºC.  add: 1µl Superscript II  mix by pipetting up and down and incubate at 42ºC for 1hour.    add: 108µl water    15µl cDNA PCR buffer   3µl dNTPs ultrapure   1µl RNase H   3µl Advantage cDNA polymerase mix  mix by pipetting up and down and run the following program:     37ºC, 5min   94ºC, 3min   65ºC, 3min   75ºC, 30min    add: 7,5µl 1M NaOH, 2mM EDTA   continue incubation at 65ºC for 10min    add  350µl water  500µl phenol:chloroform:isoamylalcohol 25:24:1  vortex vigorously for at least 30 sec. and centrifuge at 14.000 rpm for 10 min. Transfer the aqueous layer to a Microcon 100 filter column and centrifuge at 500xg for 8 min and repeat this washing step 3 times by filling up the column with water and then centrifuge again. Place column upside down into a new tube and centrifuge at 14.000xg for 1min to elute the cDNA. Dry down cDNA in a vacuum centrifuge including heat. Check the progress of drying every 10 min until the sample volume drops below ~20µl. There after, check the sample every 1-2min. Remove the sample when the volume drops to 8µl or less. If the sample volume drops to less than 8µl, add RNase free water. Continue with first round of in vitro transcription or store at -20ºC.    First round of in vitro transcription  Use Ambion T7 Mega Transcription Kit. Vortex the 10X Reaction Buffer and four ribonucleotides until they are completely in solution. Once they are thawed, store the ribonucleotides on ice, but keep the 10X Reaction Buffer at room temperature.     To 8µl cDNA add: 2µl 10X Reaction Buffer    2µl of each ribonucleotide    2µl enzyme mix  mix by pipetting up and down and incubate for 6 hours at 37ºC in an air incubator.    add:  2µl DNaseI to each reaction  mix and incubate 30min at 37ºC.      Clean the aRNA by using the GenElute kit.    add:  230µl lysis buffer (10µl β–mercapto ethanol/ml lysis buffer)    250µl 70% RNase-free EtOH  mix thoroughly by vortexing  Transfer to 500µl lysate/ethanol mixture to a binding column.  Spin 15 sec. at >12000rpm  Wash with 500µl wash solution 1  Spin 15 sec. at >12000rpm  Wash with 500µl wash solution 2  Spin 15 sec. at >12000rpm  Wash with 500µl wash solution 2  Spin 2min. at >12000rpm to remove EtOH  Transfer column to a new collection tube  Add 50µl RNase-free water  Spin 1min. at >12000rpm  (If you stop here, store aRNA at -80ºC)      Dry down aRNA in a vacuum centrifuge without heat. Check the progress of drying every 10 min until the sample volume drops below ~20µl. There after, check the sample every 1-2min. Remove the sample when the volume drops to 5µl or less. If the sample volume drops to less than 5µl, add RNase free water. Continue with second round of cDNA production or store at -80ºC.  Second round of cDNA production  combine: 5µl aRNA   4µl random hexamers  mix by pipetting up and down and incubate for 10min at 70ºC. Centrifuge briefly and place on ice.    add: 4µl first strand buffer   2µl DTT    2µl dNTP ultrapure    2µl Superscript II    1µl RNasin   mix by pipetting up and down and incubate at 42ºC for 1 hour.    add: 107µl water     15µl cDNA PCR buffer    3µl dNTPs ultrapure    1µl RNase H     3µl Advantage cDNA polymerase mix   1µl poly dT T7 primer  mix by pipetting up and down and incubate using the program:     37ºC, 2min   94ºC, 3min   65ºC, 3min   75ºC, 30min    add  7,5µl 1M NaOH, 2mM EDTA  continue incubation at 65ºC for 10min    add:  350µl water  500µl Phenol:Chloroform:Isoamyl Alcohol 25:24:1  vortex vigorously for at least 30 sec. and centrifuge at 14.000 rpm for 10 min. Transfer the aqueous layer to a Microcon 100 filter column and centrifuge at 500xg for 8 min and repeat this washing step 3 times by filling up the column with water and then centrifuge again. Place column upside down into a new tube and centrifuge at 14.000xg for 1min to elute the cDNA. Dry down cDNA in a vacuum centrifuge including heat. Check the progress of drying every 10 min until the sample volume drops below ~20µl. There after, check the sample every 1-2min. Remove the sample when the volume drops to 16µl or less. If the sample volume drops to less than 16µl, add RNase free water. Continue with second round of in vitro transcription or store at -20ºC.    Second round of in vitro transcription  Use Ambions T7 Mega Transcription Kit. Vortex the 10X Reaction Buffer and four ribonucleotides until they are completely in solution. Once they are thawed, store the ribonucleotides on ice, but keep the 10X Reaction Buffer at room temperature.     To 16µl cDNA add: 4µl 10X Reaction Buffer    4µl of each ribonucleotide    4µl enzyme mix  mix by pipetting up and down and incubate for 8 hours at 37ºC in an air incubator.    add:  2µl DNaseI to each reaction  mix and incubate 30min at 37ºC.      Clean the aRNA by using the GenElute kit.  The maximum capacity of a GenElute binding coumn is 150µg RNA. If the amplification has succeeded you should use 2 columns and elute in 2x50µl RNase free water.     add:  210µl lysis buffer (10µl β–mercaptoethanol/ml lysis buffer)    250µl 70% RNase-free EtOH  mix thoroughly by vortexing  Transfer the 500µl lysate/ethanol mixture to a binding column.  Spin 15 sec. at >12000rpm  Wash with 500µl wash solution 1  Spin 15 sec. at >12000rpm  Wash with 500µl wash solution 2  Spin 15 sec. at >12000rpm  Wash with 500µl wash solution 2  Spin 2min. to remove EtOH  Transfer column to a new collection tube  Add 2x50µl RNase-free water  Spin 1min. at >12000rpm    Take of 1.5µl for determination of concentration and quality. Store aRNA at -80ºC.    Cy-dye labeling of antisense RNA    Primer annealing:  8µg RNA   5µg random hexamers (0.5µg/µl)  RNAse free water (final volume: 15ul)  70°C 10min and cool on ice    Reverse transcription:  6µl first strand buffer  3µl DTT  1µl unlabeled dNTP mix (with less dTTP)  3µl Cy3 or Cy5 – dUTP  1µl RNasin  2µl Superscript II  2 hour at 42°C    Unlabeled dNTP mix  100mM dATP  25µl  100mM dCTP  25µl  100mM dGTP  25µl  100mM dTTP  15µl  RNase free water   76.7µl    cDNA cleanup  1. add 15µl 0.1N NaOH and incubate at 70°C for 10 min  2. add 15µl 0.1N HCL  3. add 440µl TE  4. add 15µl mouse CotI DNA  5. spin through a Microcon MP30 filter column at 13.000g for 7min  6. discard flow through, place the filter columns upside down into a new collection tube and spin for 2 min at 13.000g  7. combine probes  8. pipette probe into a new MP30 filter column and fill up with TE  9. spin for 7 min at 13.000g  (first wash)  10. discard flow through and fill up filter column with TE  11. spin for 9 min at 13.000g (second wash)  12. collect probe as in step 6  13. add 1ul (10µg/µl) yeast tRNA  14. add 1ul (10µg/µl) polyA RNA  15. dry down in speed vac if volume is larger then >5µl  16. add DIG Easy Hyb/1%BSA to a final volume of 35-40µl. Heat to 100°C for 2’ followed by 37°C for 10-15’.     Shopping list, amplification and Cy-dye labeling    • 0.5µl tubes (thin wall)  From Eppendorf. Cat. No.: 9932    • Oligo dT-T7 Primer  Custom synthesized by SGS DNA. (Superior quality synthesis and double HPLC purification.) Dissolve in RNase free water to 10µg/µl as stock and store in -20ºC.  Sequence:  5’- AAA CgA Cgg CCA gTg AAT TgT AAT ACg ACT CAC TAT Agg CgC TTT TTT TTT TTT TTT -3’    • Template Switch Oligo  Custom synthesized by SGS DNA. (Superior quality synthesis and double HPLC purification.) Dissolve in RNase

extract_protocol: For protocols concerning microvascular isolation and RNA preparation, please see Bondjers C, He L, Takemoto M, Norlin J, Asker N, Hellstrom M, Lindahl P, Betsholtz C. Microarray analysis of blood microvessels from PDGF-B and PDGF-Rbeta mutant mice identifies novel markers for brain pericytes. FASEB Journal. 2006;20(10):1703-1705.

tag: Strain

source_name: Common Reference

tag: Universal Mouse Reference RNA, cat. No.

value: 740100, Stratagene


title: 37C_42C37min

source_name: After 96h growth at 37C, RNA was collected after 37 min HS induction(42C)


title: 37C_A


title: 37C_B


title: ADULT_BRAIN_EC_MICROVASCULATURE_REPLICATE_3


title: 37C_42C15min

source_name: After 96h growth at 37C, RNA was collected after 15 min HS induction(42C)


title: 37C_42C45min

source_name: After 96h growth at 37C, RNA was collected after 45 min HS induction(42C)


title: ADULT_BRAIN_LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_1

source_name: ABLO (ADULT BRAIN LO (THE REMAINING CELLS OF THE TISSUE))


title: 37C_42C7min

source_name: After 96h growth at 37C, RNA was collected after 7 min HS induction(42C)


title: 37C_42C45min_37C10min

source_name: After 96h growth at 37C, 45min at 42 C, RNA was collected after 10 min again at 37C


title: ADULT_BRAIN_LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_3


title: ADULT_BRAIN_EC_MICROVASCULATURE_REPLICATE_2


title: EMBRYO_SKIN_EC_MICROVASCULATURE_REPLICATE_3

source_name: ESEC (EMBRYO (E18.5) SKIN EC (MICROVASCULATURE))


title: EMBRYO_SKIN_EC_MICROVASCULATURE_REPLICATE_2


title: ADULT_HEART _LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_2

source_name: AHLO (ADULT HEART LO (THE REMAINING CELLS OF THE TISSUE))


title: ADULT_HEART _EC_MICROVASCULATURE_REPLICATE_2

source_name: AHEC (ADULT HEART EC (MICROVASCULATURE))


title: EMBRYO_SKIN_LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_1

source_name: ESLO (EMBRYO (E18.5) SKIN LO (THE REMAINING CELLS OF THE TISSUE))


title: ADULT_HEART _EC_MICROVASCULATURE_REPLICATE_3


title: ADULT_HEART _EC_MICROVASCULATURE_REPLICATE_1


title: EMBRYO_SKIN_LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_3


title: EMBRYO_SKIN_LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_2


title: ADULT_HEART _LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_3


title: EMBRYO_HEART _LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_1

source_name: EHLO (EMBRYO (E18.5) HEART LO (THE REMAINING CELLS OF THE TISSUE))


title: EMBRYO_HEART _LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_3


title: EMBRYO_HEART _EC_MICROVASCULATURE_REPLICATE_1

source_name: EHEC (EMBRYO (E18.5) HEART EC (MICROVASCULATURE))


title: EMBRYO_HEART _EC_MICROVASCULATURE_REPLICATE_2


title: EMBRYO_HEART _LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_2


title: ADULT_BRAIN_LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_2


title: EMBRYO_SKIN_EC_MICROVASCULATURE_REPLICATE_1


title: ADULT_HEART _LO_THE REMAINING CELLS OF THE TISSUE_REPLICATE_1


title: EMBRYO_HEART _EC_MICROVASCULATURE_REPLICATE_3


title: 8m19_8m1

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

institute: Karolinska institutet

description: Biological replicate 1 of 4.

hyb_protocol: Cy3- and Cy5 labelled samples were purifyed and mixed before addition of a hybridization buffer and added to respectively array for 18h of hybridization. After hybridization, the slides were washed multiple times, all according to the Pronto! Plus systems and the manufacturer´s instructions (Corning and Promega).

scan_protocol: Scanning was performed using a Genepix 4200A scanner (Axon). Images were quantified using Genepix 6.0 software (Axon).

data_processing: Background was subtracted using the in-house Easy Filter software. The data was normalized by the LOWESS method using the R language. The normalized data was finally statistically analyzed using SAM.

organism: Rattus norvegicus

source_name: Fed high-fat (safflower oil) rat chow

label_protocol: 5µg of total RNA was used for a first strand cDNA synthesis of each sample, labelled with either Cy3- or Cy5-dCTP. The microarray experiment was performed using the Pronto! Plus systems according to the manufacturer´s instructions (Corning and Promega).

extract_protocol: Total RNA was extracted from frozen livers using Trizol following manufacturer's instructions

treatment_protocol: Animals were fed a short-time standard or high-fat diet before 12h of food deprivation

tag: Liver from male Sprague-Dawley rat

tag: Gender

value: male

tag: 12h of food deprivation

tag: 40 minutes of saline treatment (i.p.)

tag: Age

value: 7 weeks

tag: Tissue

value: liver

source_name: Fed standard rat chow


title: 8m18_8m3

description: Biological replicate 3 of 4.


title: 9m36_8m4

description: Biological replicate 4 of 4.

source_name: Fed high-fat (cocoa butter) rat chow


title: 8m20_8m4

description: Biological replicate 4 of 4.


title: Mouse embryo-kidney small RNA survey 18

status: Public on Dec 07 2009

type: other

city: Brisbane

first: Larry

last: Croft

state: QLD

address: The University of Queensland, St Lucia

country: Australia

institute: Institute for Molecular Bioscience

description: Survey of small RNAs (<200nt) in the mouse genome.

hyb_protocol: See the LC Sciences web page

scan_protocol: Scanner:	Axon GenePix 4000B Microarray Scanner Pixel Size:	10 µm Sample A (Cy3) Gain	450 Sample B (Cy5) Gain	485 Data Process Software:	ArrayPro Filter:	Morphological filter, Open, 3×3 Cross, 2 passes Sample A background level	305.21 Sample A background standard deviation	9.66 Sample B background level	32.46 Sample B background standard deviation	0.92 Normalization Method	Normalized to Spike-in Controls (a1, a2, and a3-PUC2PM-20B)

data_processing: Background signal was calculated from the average background probes, which contained no oligonucleotide. Signal was normalized to Spike-in Controls (a1, a2, and a3-PUC2PM-20B). The final signal value was log10 of the background corrected, normalized signal.

molecule: other

source_name: Mouse embryo 10-12 day (Ambion AM7828) size fractionated less than 200nt.

label_protocol: See the LC Sciences web page

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), then short RNAs were extracted using a Millipore centrifugal filter (YM-100) giving a size cutoff of 200 nt by the LC Sciences (Houston, TX, USA).

treatment_protocol: Ambion's Mouse Total RNAs are derived from Swiss Webster mice. Total cellular RNA is prepared using Ambion's ToTALLYTM RNA Kit (Catalog #1910) for RNA isolation. The tissues are removed, flash frozen and stored at –80°C until processing. Tissues are disrupted in liquid nitrogen to prevent degradation by endogenous nucleases. After recovery, the RNA is resuspended at 1 mg/ml in RNA Storage Solution. These RNAs have been precisely quantified, DNase-treated to minimize DNA contamination, and have been shown to be intact by functional analysis on Northern blots.

tag: Ambion FirstChoice® Mouse Total RNA embryo 10-12 day catalogue number AM7828.

tag: See the description for catalog # 7800 at Ambion

source_name: Mouse kidney (Ambion AM7826) size fractionated less than 200nt.

tag: Ambion FirstChoice® Mouse Total RNA brain catalogue number AM7826.


title: Th1-Th2-Th3 C57BL6 4

status: Public on Dec 06 2009

city: Los Angeles

first: Chaim

middle: O

last: Jacob

state: CA

address: 2011 Zonal Ave

department: Medicine/GI division

country: USA

institute: University of Southern California

scan_protocol: ABI 7900 fast real-time PCR platform

data_processing: Raw data were collected and analyzed by using SB Bioscience's superarry software.

label: SYBR Green

source_name: Mouse lymphocytes

label_protocol: QPCR SYBR Green Mix was purchased from (ABgene Inc. Rochester, New York)

extract_protocol: Total mRNA was extracted gtom each sorted cell preparation using RNA STAT-60 isolation reagents.

tag: CD4+CD44highCD62Llow/neg  cells

tag: 5 months old mice


title: Mouse embryo-testis small RNA survey 19

scan_protocol: Scanner:	Axon GenePix 4000B Microarray Scanner Pixel Size:	10 µm Sample A (Cy3) Gain	470 Sample B (Cy5) Gain	510 Data Process Software:	ArrayPro Filter:	Morphological filter, Open, 3×3 Cross, 2 passes Sample A background level	240.66 Sample A background standard deviation	8.31 Sample B background level	37.91 Sample B background standard deviation	1.94 Normalization Method	Normalized to Spike-in Controls (a1, a2, and a3-PUC2PM-20B)

source_name: Mouse testis (Ambion AM7822) size fractionated less than 200nt.

tag: Ambion FirstChoice® Mouse Total RNA testicle catalogue number AM7822.


title: Th1-Th2-Th3 C57BL6 1


title: Th1-Th2-Th3 p55/p75 DKO 3


title: Th1-Th2-Th3 C57BL6 3


title: 8m17_8m2

description: Biological replicate 2 of 4.


title: Th1-Th2-Th3 C57BL6 2


title: TH17 C57BL6 2


title: 9m34_8m2

description: Biological replicate 2 of 4.


title: Th1-Th2-Th3 p55/p75 DKO 4


status: Public on Dec 09 2009

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from hydrogen producing cells of E. coli BW25113 fhlA/pCA24N-FhlA after 30 min. of anaerobic incubation in modified-complex 20 mM formate at 37ºC

hyb_protocol: Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: BW25113 fhlA/pCA24N-FhlA

label_protocol: cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: 1 mL of overnight culture in modified - complex 20 mM formate + Cm 30 µg/mL was inoculated in 9 mL of fresh modified - complex 20 mM formate + Cm 30 µg/mL and incubated anaerobically at 37oC for 30 minutes in 27 mL glass vials. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)


title: 9m33_8m1

description: Biological replicate 1 of 4.


title: Mouse embryo-ovary small RNA survey 20

scan_protocol: Scanner:	Axon GenePix 4000B Microarray Scanner Pixel Size:	10 µm Sample A (Cy3) Gain	455 Sample B (Cy5) Gain	480 Data Process Software:	ArrayPro Filter:	Morphological filter, Open, 3×3 Cross, 2 passes Sample A background level	186.82 Sample A background standard deviation	6.47 Sample B background level	37.31 Sample B background standard deviation	2.45 Normalization Method	Normalized to Spike-in Controls (a1, a2, and a3-PUC2PM-20B)

source_name: Mouse ovary (Ambion AM7824) size fractionated less than 200nt.

tag: Ambion FirstChoice® Mouse Total RNA ovary catalogue number AM7824.


title: TH17 C57BL6 3


title: BW25113 fhlA/pCA24N-FhlA133 after 30 min. of anaerobic incubation in modified-complex 20 mM formate at 37ºC

description: RNA extracted from hydrogen producing cells of E. coli BW25113 fhlA/pCA24N-FhlA133 (Q11H, L14V, Y177F, K245R, M288K, and I342F)after 30 min. of anaerobic incubation in modified-complex 20 mM formate at 37ºC

source_name: BW25113 fhlA/pCA24N-FhlA133


title: Mouse embryo-lung small RNA survey 21

scan_protocol: Scanner:	Axon GenePix 4000B Microarray Scanner Pixel Size:	10 µm Sample A (Cy3) Gain	475 Sample B (Cy5) Gain	480 Data Process Software:	ArrayPro Filter:	Morphological filter, Open, 3×3 Cross, 2 passes Sample A background level	271.19 Sample A background standard deviation	9.23 Sample B background level	35.76 Sample B background standard deviation	2.01 Normalization Method	Normalized to Spike-in Controls (a1, a2, and a3-PUC2PM-20B)

source_name: Mouse lung (Ambion AM7818) size fractionated less than 200nt.

tag: Ambion FirstChoice® Mouse Total RNA lung catalogue number AM7818.


title: TH17 C57BL6 1


title: Prostate_epithelial_cell_line_PPARg_knockout

city: Nashville

first: Simon

last: Hayward

state: TN

department: Urologic Surgery

institute: Vanderbilt University Medical Center

description: To investigate global gene expression profiling in both of PPARg-deficient mouse prostate epithelial cells, mPrE-PPARg knockout (mPrE-gKO) and mPrE-PPARg2 shRNA (mPrE-g2sh). The mPrE-PPARg knockout and mPrE-PPARg2 shRNA cells were compared to wildtype mPrE cells.

hyb_protocol: Dried-down targets were then resuspended in 50ul of MWG Hyb Buffer (Ocimum Biosolutions, cat#1180-200000) and 1 ug of Poly A RNA (Sigma, P9403) was added to each target. The targets were heat denatured and then hybridized 16 hours at 42C on a Maui Hyb Station (BioMicro Systems, Inc., 4 chamber model).  Immediately prior to hybridization, the microarrays were first vigorously dunked in a 0.2% SDS solution at room temp followed by  prehybridization in a solution of 5x SSC, 1% SDS, and 1% BSA at 55° C for 60 minutes.  Following prehybridization, the arrays were vigorously washed in 9 exchanges of ddH2O to remove all traces of the prehybridization solution, rinsed in isopropanol, and dried at room temperature.  The target samples were denatured at 95°C for three minutes and placed on the prehybridized arrays, covered with specialized hybridization chambers from BioMicro Inc (Salt Lake City, UT).  Arrays were hybridized using the MAUI hybridization system (BioMicro) for 16 hours at 42° C using the manufacturer’s mixing protocol “B”.  After hybridization, the arrays were washed in 2X SSC/0.1% SDS at 55° C with agitation for 5 minutes then washed with two successive 5 minute washes with 1x SSC and 0.1xSSC at RT.  The washed arrays were dried by centrifugation at 50xg for 5 minutes and immediately scanned using a GenePix 4000B microarray scanner [Axon Instruments, Union City, CA].

data_processing: Raw data was loaded into GeneSpring (v.7) [Agilent Technologies, Inc.] using GenePix-format defaults. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. After normalization, all data was filtered to eliminate all data points that may not be reliable. This included flagged spots, lowly expressed spots (signal less than 200), and spots with negative signal values. After filtering, the genes were chosen for further analysis on the basis of fold change of treated samples vs. controls (2 and higher up- or down-regulation) in 2 or 3 experiments with P value of less than0.05. Finally, Excel file was created for genes representing proteins with specific molecular functions (e.g., transcriptional factors) or  known to be involved in different cellular processes (e.g., apoptosis).

source_name: PPARg knockout mouse prostate epithelial cell line

label_protocol: Briefly, 5-10 ug of total RNA from each sample were reverse transcribed using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA).  Generated cDNA targets were purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA). The purified cDNA targets were dried to completion and then differentially coupled to ester-linked Cy3 (controls) or Cy5 (LiCl-treated) dye (Amersham, Piscataway, NJ). After quenching of unbound dye with 4M Hydroxylamine, Cy3- and Cy5-labeled cDNA target pairs were combined and cleaned up over QIAquick columns (Qiagen, Valencia, CA).

growth_protocol: The wildtype mPrE, mPrE-PPARg knockout and mPrE-PPARg2 shRNA cells were growed in growth medium (RPMI1640 with 5% FBS and 1% Am/Ab)for three days in T-75 cm2 flasks. Cells were harvested on day 3 at 70-80% confluency using QIAGEN kit for isolation of total RNA.

extract_protocol: Total RNA was isolated from three cell lines growing in T-75 cm2 flasks for three days by using RNeasy Mini Kit (Qiagen, Valencia, CA) and RNase-Free DNase Set (Qiagen, Valencia, CA) according to the manufacturer’s instructions. To elute RNA from columns at final elution, 30-40 ul water were used to get about 30-50 ug total RNA.

treatment_protocol: no treatment

value: 6 months

value: prostate tissues

source_name: wild-type mouse prostate epithelial cell line


title: Mouse embryo-brain small RNA survey 17

scan_protocol: Scanner:	Axon GenePix 4000B Microarray Scanner Pixel Size:	10 µm Sample A  (Cy3) Gain	500 Sample B  (Cy5) Gain	520 Data Process Software:	ArrayPro Filter:	Morphological filter, Open, 3×3 Cross, 2 passes Sample A background level	560.63 Sample A background standard deviation	12.76 Sample B background level	36.05 Sample B background standard deviation	1.30 Normalization Method	Normalized to Spike-in Controls (a1, a2, and a3-PUC2PM-20B)

source_name: Mouse brain (Ambion AM7812) size fractionated less than 200nt.

tag: Ambion FirstChoice® Mouse Total RNA brain catalogue number AM7812.


title: Th1-Th2-Th3 p55/p75 DKO 2


title: Th1-Th2-Th3 p55/p75 DKO 1


title: TH17 p55/p75 DKO 2


title: Prostate_epithelial_cell_line_PPARg2_knockdown

scan_protocol: The washed arrays were dried by centrifugation at 50xg for 5 minutes and immediately scanned using a GenePix 4000B microarray scanner [Axon Instruments, Union City, CA].

source_name: mouse prostate epithelial cell line with PPARg2 knockdown

tag: Strain

source_name: mouse prostate epithelial cell line with pSIR empty vector-transfected


title: TH17 p55/p75 DKO 1


title: liver_ob/ob mouse-9

status: Public on Dec 04 2009

city: Hangzhou

first: Shengjie

last: Li

address: 79 Qingchun Road

country: China

institute: the First Affiliated Hospital of Zhejiang University School of Medicine

description: Purified RNA was labeled with fluorescein and hybridization was carried out on the CapitalBio Mammalian miRNA Array V 3.0 containing 509 probes in triplicate, corresponding to 435 human and mouse mature miRNA genes.

hyb_protocol: After 2 hours, the labeled RNA was precipitated and resuspended in 15% formamide, 0.2% SDS, 3xSSC and 50xDenhardt's. The sample was hybridized on array slides overnight at 42C. The  slides were washed by incubating 4 minutes in 0.2% SDS, 2xSSC at 42C, and 4 minutes in 0.2xSSC at room temprature.

scan_protocol: Processed slides were scanned using a LuxScan 10K/A Microarray Scanner (CapitalBio Corp., Beijing, China).The scanning setting is adjusted to obtain an equal visualized intensity of U6 spots across arrays.

data_processing: Data analysis from the obtained TIFF images is performed using SpotData Pro software (CapitalBio Corp). The quantified signal intensity values of microarray were normalized to per-chip mean values and 2-scale log-transformed.

source_name: liver, ob/ob mouse

label_protocol: 50μg total RNA was purified using mirVANA miRNA isolation kit (Ambion, Inc.) to enrich small RNA fraction. Purified RNA was 3'-end labeled with Cy3 dinucleotides using T4 RNA ligase by incubating on ice.

extract_protocol: Frozen liver tissues were dissected and homogenized and total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: female

tag: Age:12 weeks

tag: Animal model

value: non-alcoholic fatty liver disease


title: liver_ob/ob mouse-10

tag: Gender


title: liver_STZ-induced diabetic mouse-8

source_name: liver, STZ-induced diabetic mouse

value: 8 weeks

value: STZ-induced type 8 diabetes mellitus


title: liver_STZ-induced diabetic mouse-7

value: STZ-induced type 7 diabetes mellitus


title: liver_STZ-induced diabetic mouse-5

value: STZ-induced type 5 diabetes mellitus


title: liver_STZ-induced diabetic mouse-4

value: STZ-induced type 4 diabetes mellitus


title: liver_ob/ob mouse-5

value: 11 weeks


title: liver_ob/ob mouse-6


title: liver_ob/ob mouse-8


title: Hducreyi_FCS_Rep2

status: Public on Dec 05 2009

city: Dallas

first: Eric

middle: J

last: Hansen

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Equal amounts of labeled cDNA from cells grown under both conditions were thoroughly mixed and used to hybridize microarray slides in the hybridization buffer provided with the CyScribe Post-Labeling kit (GE Healthcare). Hybridization was carried out at 50°C for 16 h in the dark.

scan_protocol: After hybridization, the slides were washed in saline-sodium phosphate-EDTA buffer and scanned with GenePix scanner 4100A and GenePix Pro 5.0 software (Axon Instruments Inc.).

data_processing: Data was subjected to two types of normalization, a ratio-based normalization so that the mean or median intensities are the same across the array, and a non-linear locally-weighted scatterplot smoothing (LOWESS) normalization, which corrects intensity-dependent variation in dye bias, before being combined into a single data set for further analysis. Differential expression was defined as a minimum of two fold over or under expression in the cells grown in CB+FCS relative to cells grown in CB-FCS.  The data were further scrutinized so as to only include expression profiles that were observed in at least three of the four experiments and had a P≤0.05 after one sample t-test analysis.

organism: [Haemophilus] ducreyi 35000HP

source_name: H. ducreyi 35000HP, +FCS

label_protocol: Twenty micrograms of total RNA from cells grown in CB+FCS for 8 hrs, were used to generate cDNA with the Amino Allyl cDNA Labeling Kit (Ambion). After reverse transcription, residual RNA was removed by alkaline treatment, followed by neutralization. The cDNAs were purified using the QIAquick gel extraction kit (QIAGEN). After purification, Cy5 dye (GE Healthcare) was added following manufacturer's instructions. The labeled cDNAs were cleaned by using YM-30 Microcon centrifugal filter devices (Millipore) and labeling efficiency and concentration was determined using a NanoDrop spectophotometer.

extract_protocol: Stop buffer (200 mM Tris.Cl pH8, 20nM EDTA pH 8 and 20mM sodium azide) was added to 5-10 ml bacteria prior to collection by centrifugation.  Total RNA was extracted using the RiboPure™ Kit (Ambion) following the manufacturer's instructions. After isolation, RNA was treated twice with DNaseI (Ambion) for 1 hr at 37°C, and purified using the RNeasy system (Qiagen).  Samples were checked for residual DNA by PCR and re-treated with DNAseI if necessary.

treatment_protocol: Wild-type H. ducreyi strains were resuscitated from frozen stock on chocolate agar (CA) plates, and incubated at 33°C in a humidified atmosphere containing 95% air and 5% CO2 .  Strains were grown at 33°C in a gyratory water bath at 100 rpm in a Columbia broth-based medium (35 g of Columbia broth (Difco) per liter, 0.1% (wt/vol) Trizma base (Sigma), equine hemin (25 µg/ml; Sigma), 1% (vol/vol) IsoVitaleX (Becton Dickinson)) with 2.5% (vol/vol) heat-inactivated fetal calf serum (FCS).

tag: Haemophilus ducreyi 35000HP grown in Columbia broth supplemented with 2.5% FCS, for 8 hours.

source_name: H. ducreyi 35000HP, -FCS

label_protocol: Twenty micrograms of total RNA from cells grown in CB-FCS for 8 hrs, were used to generate cDNA with the Amino Allyl cDNA Labeling Kit (Ambion). After reverse transcription, residual RNA was removed by alkaline treatment, followed by neutralization. The cDNAs were purified using the QIAquick gel extraction kit (QIAGEN). After purification, Cy3 dye (GE Healthcare) was added following manufacturer's instructions. The labeled cDNAs were cleaned by using YM-30 Microcon centrifugal filter devices (Millipore) and labeling efficiency and concentration was determined using a NanoDrop spectophotometer.

treatment_protocol: Wild-type H. ducreyi strains were resuscitated from frozen stock on chocolate agar (CA) plates, and incubated at 33°C in a humidified atmosphere containing 95% air and 5% CO2 .  Strains were grown at 33°C in a gyratory water bath at 100 rpm in a Columbia broth-based medium (35 g of Columbia broth (Difco) per liter, 0.1% (wt/vol) Trizma base (Sigma), equine hemin (25 µg/ml; Sigma), and 1% (vol/vol) IsoVitaleX (Becton Dickinson)).

tag: Haemophilus ducreyi 35000HP grown in Columbia broth for 8 hours.


title: liver_STZ-induced diabetic mouse-2

tag: Age

value: STZ-induced type 2 diabetes mellitus


title: liver_STZ-induced diabetic mouse-3

value: STZ-induced type 3 diabetes mellitus


title: Hducreyi_FCS_Rep1

tag: H. ducreyi 35000HP grown in Columbia broth for 8 hours.

tag: H. ducreyi 35000HP grown in Columbia broth supplemented with 2.5% FCS, for 8 hours.


title: liver_STZ-induced diabetic mouse-1

value: STZ-induced type 1 diabetes mellitus


title: liver_ob/ob mouse-4


title: liver_STZ-induced diabetic mouse-6

value: STZ-induced type 6 diabetes mellitus


title: liver_ob/ob mouse-7


title: liver_normal C57BL/6 mouse-4

source_name: liver, C57BL/6 mouse

value: male

value: normal control


title: liver_normal C57BL/6 mouse-6


title: Hducreyi_FCS_Rep4


title: liver_ob/ob mouse-1


title: liver_ob/ob mouse-2


title: liver_ob/ob mouse-3


title: liver_normal C57BL/6 mouse-5


title: liver_normal C57BL/6 mouse-1


title: liver_normal C57BL/6 mouse-7


title: liver_normal C57BL/6 mouse-2


title: 9m35_8m3

description: Biological replicate 3 of 4.

source_name: Fed high-fat (cocoa butter) rat chow

tag: Liver from male Sprague-Dawley rat

tag: 12h of food deprivation

tag: 40 minutes of saline treatment (i.p.)

value: 7 weeks

tag: Tissue

value: liver

source_name: Fed standard rat chow


title: liver_normal C57BL/6 mouse-8


title: Hducreyi_FCS_Rep3


title: liver_normal C57BL/6 mouse-3


title: TH17 p55/p75 DKO 3

source_name: Mouse lymphocytes

tag: CD4+CD44highCD62Llow/neg  cells

tag: 5 months old mice


title: Berry_mature_1

status: Public on Dec 02 2009

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

description: All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 1% SDS, 0.2% BSA) for 60 minutes at 37 °C. Hybridization was performed at 37°C for 16 hours in hybridization solution (6X SSPE, 0.8% BSA, 12% DI Formamide, 2.5% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - 2 washes with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).

scan_protocol: Scanning was performed using Perkin Elmer ScanArray 4000XL microarray scanner and ScanArray Express 4.0 acquisition software. Laser was set at 60% of power. PMT gain was set at 60%.

data_processing: Raw data was extracted using Microarray Imager 5.8.0 software (Combimatrix). Data were quantile-normalized using Blist 0.6 software (Combimatrix).

organism: Vitis vinifera

source_name: Pool of mature berries

label_protocol: 3 ug of low molecular weight RNA were labeled with Cy5 (Mirus LabelIT miRNA labeling Kit (Mirus Bio Corp.) following manufacturer instructions.

extract_protocol: In order to isolate low molecular weight RNA, total RNA was extracted from V. vinifera L. cv Corvina tissues and size fractioned, following the procedure described by Carra et al., 2007 (doi:10.1016/j.ab.2006.09.022). Before extracting RNA from berries, seeds were separated from the rest of the fruit.

tag: Cultivar

value: Corvina


title: Berry_preveraison_2

source_name: Pool of berries at preveraison stage


title: Berry_veraison_2

source_name: Pool of berries at veraison stage


title: Inflorescence_young_1

source_name: Inflorescence at early stages of development


title: Berry_veraison_1


title: Berry_mature_2


title: Roots_1

source_name: Pool of grape roots


title: Inflorescence_young_2


title: Berry_preveraison_1


title: Leaves_pool_1

source_name: Leaves pool


title: Leaves_pool_2


title: Roots_2


title: CRT knockout mouse embryonic stem cell, biological rep5

city: Rochester

first: Randolph

last: Faustino

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description: Gene expression data from murine embryonic stem cells with calreticulin deficiency

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

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

source_name: Calreticulin knockout of mouse embryonic stem cell line

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

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

value: D3, mouse embryonic stem cell


title: CRT knockout mouse embryonic stem cell, biological rep3


title: CRT knockout mouse embryonic stem cell, biological rep2


title: CRT knockout mouse embryonic stem cell, biological rep4


title: CRT knockout mouse embryonic stem cell, biological rep1


title: Wild type mouse embryonic stem cell, biological rep2

description: Gene expression data from wild type murine embryonic stem cells

source_name: Wild type mouse embryonic stem cells


title: 251485028602_1

status: Public on Dec 01 2009

city: Baltimore

first: Jin

last: Song

state: MD

address: 419 N. Caroline Str.

department: Pathology

institute: Johns Hopkins Medical Institutions

hyb_protocol: Total 0.825 µg of each Cy3-labeled sample was used for hybridization on Agilent 4x 44K whole human genome microarray at 65ºC for 17 hours in a hybridization oven with rotation.

scan_protocol: Slides were scanned using the Agilent Microarray Scanner controlled by Agilent Scan Control 7.0 software.

data_processing: Microarray data were extracted with Agilent Feature Extraction 9.5.3.1 software and imported into GeneSpring GX 9.0.1 (Agilent). Normalization was done with all intensities higher than 5, log2 transformation and cross-array quartile normalization. Features with intensities smaller than 300 at all time points were excluded from the analysis.

organism: Homo sapiens

source_name: ovarian cancer cell line

label_protocol: Total RNA was labeled using Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent) following the manufacturer’s instruction with minor modifications. Briefly, 0.4 µg RNA was reverse-transcribed into cDNA by MMLV-RT using an oligo dT primer (System Biosciences) that incorporated a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-3 labeled CTPs (Perkin Elmer). RNA spike-in controls (Agilent) were added to RNA samples before amplification and labeling. The labeled cRNA was purified using RNeasy mini kit (Qiagen).

extract_protocol: Total RNA was isolated using TRIZOL reagent (Invitrogen) followed by RNeasy mini kit with DNase on-column digestion (Qiagen). RNA was quantified with NanoDrop ND-1000 followed by quality assessment with the 2100 Bioanalyzer (Agilent) according to manufacturer’s protocol

tag: 0 hours


title: 251485028602_4

tag: 24 hours


title: 251485028601_4


title: 251485028602_2

tag: 8 hours


title: 251485028602_3

tag: 16 hours


title: Moniezia expansa and Moniezia benedini(immuture 2)

city: Shi Hezi

first: Wenjuan

last: Zhao

state: Xinjiang

address: Wu Yi Road 221#

institute: The Breed & Biotechnology Key Laboratory of Sheep in XinJiang Bingtuan

description: Immature proglottids of Moniezia benenidi tissue versus scolex-neck proglottids of Moniezia expansa tissue reference.

hyb_protocol: The probe was dissolved in 20 ml of hybridization solution (5×SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide). Microarrays were pre-hybridized with a hybridization solution containing 0.5 mg/ml of denatured salmon sperm DNA at 42℃ for 6 h. Fluorescent probe mixtures were denatured at 95℃ for 5 min and then applied onto the pre-hybridized chip under a cover glass. Chips were hybridized at 42℃ for 15–17 h. Next, the hybridized chips were each washed at 60℃ for 10 min in solutions of 2×SSC and 0.2% SDS, 0.1×SSC and 0.2% SDS, 0.1×SSC and then dried at room temperature.

scan_protocol: The chips were scanned with a ScanArray 4000 (GSI Lumonics, Bellerica, MA, USA) at two wavelengths, 635 and 532 nm, to detect emission from both Cy5 and Cy3, respectively.

data_processing:
VALUE is the normalized ratio of the median of Channel 1 (635 nm) to Channel 2 (532 nm) using LOWESS strategy.
Only genes with raw intensity values for both Cy3 and Cy5 of >200 were chosen for differential analysis. Genes were identified as differentially expressed if the ratio was >2 or <0.5, or the absolute value of base 2 logarithm of the ratio was >1 or < -1.

organism: Moniezia benedeni

source_name: immature proglottids of Moniezia benedini

label_protocol: The fluorescent cDNA probes were prepared through reverse transcription of the isolated mRNAs and then purified. The RNA samples from Moniezia expansa mature proglottids tissue was labeled with Cy5-dUTP.

extract_protocol: Immature proglottids from 3 moniezia benedini were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and then were homogenized in TRIzol (GibcoBRL, Grand Island, NY). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol for 10 min at 4°C. Pellet the RNA by centrifugation for 10min at 4°C in a microcentrifuge. Carefully pour off the isopropanol without dislodging the RNA pellet. Remove all of the residual isopropanol with a pipet and dissolve RNA in Milli-Q H2O

tag: Just behind the neck are the immature proglottids, contain immature female and male organs.

organism: Moniezia expansa

source_name: scolex neck of Moniezia expansa

label_protocol: The fluorescent cDNA probes were prepared through reverse transcription of the isolated mRNAs and then purified. The RNA samples from scolex-neck proglottids mixed tissue were labeled with Cy3-dUTP.

extract_protocol: 6 Moniezia expansa scolex-neck proglottidstissue were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and then were homogenized in TRIzol (GibcoBRL, Grand Island, NY). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol for 10 min at 4°C. Pellet the RNA by centrifugation for 10min at 4°C in a microcentrifuge. Carefully pour off the isopropanol without dislodging the RNA pellet. Remove all of the residual isopropanol with a pipet and dissolve RNA in Milli-Q H2O.

tag: The scolex is very small (mostly less than 1 mm) and endowed with specific holdfast systems such as acetabula and hooks. The small neck region is the continuously differentiating zone that produces immature proglottids.


title: 251485028601_1


title: 251485028601_3


title: Moniezia expansa_immature proglottids_2

description: Moniezia expansa immature proglottids tissue versus scolex-neck proglottids tissue reference

scan_protocol: The chips were scanned with a ScanArray 4000 (GSI Lumonics, Bellerica, MA, USA) at two wavelengths, 635 and 532 nm, to detect emission from both Cy5 and Cy3, respectively. The acquired images were analyzed using GenePix Pro 3.0 software.

label_protocol: The fluorescent cDNA probes were prepared through reverse transcription of the isolated mRNAs and then purified. The RNA samples from Moniezia expansa  mature proglottids tissue was labeled with Cy5-dUTP.

extract_protocol: immature proglottids from 3 moniezia expansas were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and then were homogenized in TRIzol (GibcoBRL, Grand Island, NY). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol for 10 min at 4°C. Pellet the RNA by centrifugation for 10min at 4°C in a microcentrifuge. Carefully pour off the isopropanol without dislodging the RNA pellet. Remove all of the residual isopropanol with a pipet and dissolve RNA in Milli-Q H2O

tag: Just behind the neck are the immature proglottids, contain immature female and male organs

source_name: Moniezia expansa scolex-neck proglottids tissue

label_protocol: The fluorescent cDNA probes were prepared through reverse transcription of the isolated mRNAs and then purified. The RNA samples from scolex-neck proglottids mixed tissue were labeled with Cy3-dUTP

tag: The scolex is very small (mostly less than 1 mm) and endowed with specific holdfast systems such as acetabula and hooks. The small neck region is the continuously differentiating zone that produces immature proglottids


title: 251485028601_2


title: Moniezia expansa and Moniezia benedini(immature 1)


title: Moniezia expansa and Moniezia benedini(gravid 1)

description: gravid proglottids of Moniezia benenidi tissue versus scolex-neck proglottids of Moniezia expansa tissue reference.

source_name: gravid proglottids of Moniezia benedini

extract_protocol: Gravid proglottids from 3 moniezia benedini were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and then were homogenized in TRIzol (GibcoBRL, Grand Island, NY). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol for 10 min at 4°C. Pellet the RNA by centrifugation for 10min at 4°C in a microcentrifuge. Carefully pour off the isopropanol without dislodging the RNA pellet. Remove all of the residual isopropanol with a pipet and dissolve RNA in Milli-Q H2O

tag: uterus contains fertilized eggs, procreation organs degenerate even disappeared


title: Moniezia expansa_mature proglottids_1

description: Moniezia expansa mature proglottids tissue versus scolex-neck proglottids tissue reference

extract_protocol: mature proglottids from 3 moniezia expansas were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and then were homogenized in TRIzol (GibcoBRL, Grand Island, NY). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol for 10 min at 4°C. Pellet the RNA by centrifugation for 10min at 4°C in a microcentrifuge. Carefully pour off the isopropanol without dislodging the RNA pellet. Remove all of the residual isopropanol with a pipet and dissolve RNA in Milli-Q H2O

tag: contain mature female and male organs

tag: scolex-neck proglottids

value: The scolex is very small (mostly less than 1 mm) and endowed with specific holdfast systems such as acetabula and hooks. The small neck region is the continuously differentiating zone that produces immature proglottids


title: Wild type mouse embryonic stem cell, biological rep1

tag: Strain


title: Moniezia expansa_mature proglottids_2

source_name: Moniezia expansa mature proglottids tissue


title: Moniezia expansa_immature proglottids_1

source_name: Moniezia expansa immature proglottids tissue


title: Moniezia expansa and Moniezia benedini (mature 2)

description: Mature proglottids of Moniezia benenidi tissue versus scolex-neck proglottids of Moniezia expansa tissue reference.

source_name: mature proglottids of Moniezia benedini

extract_protocol: Mature proglottids from 3 moniezia benedini were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and then were homogenized in TRIzol (GibcoBRL, Grand Island, NY). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol for 10 min at 4°C. Pellet the RNA by centrifugation for 10min at 4°C in a microcentrifuge. Carefully pour off the isopropanol without dislodging the RNA pellet. Remove all of the residual isopropanol with a pipet and dissolve RNA in Milli-Q H2O

tag: Glands of Moniezia benedini arranged in a linear pattern and mature proglottids of Moniezia benedini contains two sets of sexual organs.


title: Moniezia expansa_gravid proglottids_1

description: Moniezia expansa gravid proglottids tissue versus scolex-neck proglottids tissue reference

extract_protocol: gravid proglottids from 3 moniezia expansas were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and then were homogenized in TRIzol (GibcoBRL, Grand Island, NY). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol for 10 min at 4°C. Pellet the RNA by centrifugation for 10min at 4°C in a microcentrifuge. Carefully pour off the isopropanol without dislodging the RNA pellet. Remove all of the residual isopropanol with a pipet and dissolve RNA in Milli-Q H2O


title: Moniezia expansa and Moniezia benedini(mature 1)


title: Moniezia expansa_gravid proglottids_2

source_name: Moniezia expansa gravid proglottids tissue


title: Moniezia expansa and Moniezia benedini(gravid 2)

source_name: gravid proglottids tissue of Moniezia benedini

tag: uterus contains fertilized eggs, procreation organs degenerate even disappeared.


title: Inter-nodal stem, 15 days after callus induction, prior to shoot induction, biological replicate B

city: Corvallis

first: Yanghuan

last: Bao

state: OR

address: Department of Forest Science, Oregon State University, 321 Richardson Hall

department: Forest Science, and Genetics

institute: Oregon State University

description: Gene expression data from poplar inter-nodal stem segements prior to transfering to Shoot Induction Medium (15 days on CIM)

hyb_protocol: Labeling, Hybridization and Scanning Protocols followed are from the  GeneChip® Expression Analysis Technical Manual ( 701021 Rev. 5)

data_processing: The probe-level data were normalized by the GC Robust Multichip Average (GCRMA) algorithm using affylmGUI.

organism: Populus tremula x Populus alba

growth_protocol: Plants were in vitro propagated according to published protocols - Meilan R, Ma C: Poplar (Populus spp.) Methods Mol Biol JT - Methods in molecular biology (Clifton, NJ) 2006, 344:143-151.

extract_protocol: Total RNA was isolated and purified according to the RNeasy Mini Protocol for Isolation of Total RNA from Plant Cells and Tissues and Filamentous Fungi (QIAGEN Inc., Valencia, CA).

treatment_protocol: Inter-nodal stem segments (3-4 mm in length) from in vitro micropropagated plants were cut and incubated on callus induction medium (CIM) for 15 days, and then were transferred to shoot induction medium (SIM)

tag: INRA 717-1 B4, Populus tremula x P. alba

tag: Gender

value: female


title: Inter-nodal stem, shoot induction, 8 days, biological replicate B

description: Gene expression data from poplar inter-nodal stem segements 8 days on Shoot Induction Medium (SIM)

scan_protocol: Labeling, Hybridization and Scanning Protocols followed are from the  GeneChip® Expression Analysis Technical Manual ( 701021 Rev. 5)


title: Inter-nodal stem, shoot induction, 3 days, biological replicate B

description: Gene expression data from poplar inter-nodal stem segements 3 days on Shoot Induction Medium (SIM)

label_protocol: Labeling, Hybridization and Scanning Protocols followed are from the  GeneChip® Expression Analysis Technical Manual ( 701021 Rev. 5)


title: Inter-nodal stem, prior to callus induction, biological replicate B

description: Gene expression data from poplar inter-nodal stem segements prior to callus induction


title: Inter-nodal stem, callus induction, 3 days, biological replicate B

description: Gene expression data from poplar inter-nodal stem segements 3 days on Callus Induction Medium (CIM)


title: Inter-nodal stem, 15 days after callus induction, prior to shoot induction, biological replicate A


title: Inter-nodal stem, callus induction, 3 days, biological replicate A


title: Inter-nodal stem, shoot induction, 3 days, biological replicate A


title: Inter-nodal stem, shoot induction, 8 days, biological replicate A


title: Inter-nodal stem, prior to callus induction, biological replicate A


title: Adult testes pool 1

city: Praha

first: Libor

last: Morkovsky

address: Vinicna 7

department: Department of zoology

country: Czech Republic

institute: Charles University in Prague

description:
Inbred CB congenic lines derived from White Leghorn were used as donors of tissues. 17 weeks old individuals were dissected and their gonads were frozen in liquid nitrogen and stored at -80 °C prior to RNA isolation. All animals were maintained at the Institute of Molecular Genetics (Prague, Czech Republic).
pool of testes from 4 individuals

hyb_protocol: standard Affymetrix Expression protocol, 45°C, 60 rpm, 16 hours, Affymetrix Hybridization Oven 640. Performed at Microarray Core Facility at the Institute of Molecular Genetics (Prague, Czech Republic).

scan_protocol: standard Affymetrix Expression protocol, stained in Fludics Station 450, scanned in GeneChip Scanner 3000 7G controlled by GCOS 1.4. Performed at Microarray Core Facility at the Institute of Molecular Genetics (Prague, Czech Republic).

data_processing: gcRMA in BioConductor, MAS5 absent/present calls implementation in BioConductor

label: Biotin

organism: Gallus gallus

source_name: testes, whole tissue

label_protocol: Standard Affymetrix Expression protocol, 5 ug total RNA. Performed at Microarray Core Facility at the Institute of Molecular Genetics (Prague, Czech Republic).

extract_protocol: Trizol Reagent (Invitrogen), according to the manufacturer's protocol. Tissue homogenization was performed by a handheld rotor-stator type of homogenizer. RNA concentration was determined spectrophotometrically at A260nm by NanoDrop (NanoDrop Technologies) and the integrity was checked on Agilent 2100 bioanalyser - RNA Lab-On-a-Chip (Agilent Technologies). Total RNA from gonads of 8 males and 8 females was used for hybridization to Affymetrix GeneChip® Chicken Genome Arrays. Prior to hybridization the samples were combined in equal quantities into 4 pools (4 testes/ovary samples in each pool), 2 of them representing testis and 2 ovary.

tag: Inbred CB congenic line derived from White Leghorn, 17 weeks old, males


title: Adult ovary pool 2

description:
Inbred CB congenic lines derived from White Leghorn were used as donors of tissues. 17 weeks old individuals were dissected and their gonads were frozen in liquid nitrogen and stored at -80 °C prior to RNA isolation. All animals were maintained at the Institute of Molecular Genetics (Prague, Czech Republic).
pool of ovaries from 4 individuals

source_name: ovary, whole tissue

tag: Inbred CB congenic line derived from White Leghorn, 17 weeks old, females


title: PBMC_Fed_Con_7

city: Wageningen

first: Jaap

last: Keijer

state: gld

address: Marijkeweg 40

department: Human and Animal Physiology

country: Netherlands

institute: Wageningen University

description: Diet induced gene expression in rat peripheral blood mononuclear cells

hyb_protocol: Hybridization was performed by preparing a 2x cRNA target solution containing 825 ng Cy5-labeled cRNA, 825 ng Cy3-labeled pool cRNA and 11 µL 10x blocking agent in a total volume of 52.8 µL. Then 2.2 µL fragmentation buffer was added and incubated at 60°C for 30 min. Fragmentation was stopped by adding 55 µL 2x GEx hybridization buffer HI-RPM and hybridized on 4x 44K G4131F whole genome Agilent arrays (Agilent Technologies, Inc. Santa Clara, CA) for 17 h at 65°C in Agilent hybridization chambers in an Agilent hybridization oven rotating at 10 rpm. After hybridization the arrays were subsequently washed with ‘GE wash buffer 1’ for 1 min at room temperature, ‘GE wash buffer 2’ for 1 min at approximately 37°C, acetonitrile for 1 min at room temperature and 30 s at room temperature with ‘stabilization and drying solution’ according to manufacturers protocol (Agilent Technologies).

scan_protocol: Arrays were scanned with an Agilent Microarray Scanner (Agilent Technologies). Spot intensities were quantified using Feature extraction 8.5 (Agilent Technologies).

data_processing: Median density values and background values of each spot were extracted for both the experimental samples (Cy5) and the reference samples (Cy3). Data was exported into GeneMaths XT (Applied Maths, Sint-Martens-Latem, Belgium) for analysis. Spots with an average Cy5 signal intensity, over all arrays, lower than 2-fold average Cy5 local background were discarded. Subsequently, the remaining Cy5 signal intensities were normalized against the Cy3 reference using RIKILT normalization protocol (Pellis L, et al. (2003) Physiol Genomics 16: 99-106).

source_name: PBMC, Fed, Control,  7

label_protocol: 0.5 μg RNA of each sample was reverse transcribed using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent), according to the manufacturer’s protocol (all materials and reagents are from Agilent Technologies, Palo Alto, CA, USA unless stated otherwise). Half of the cDNA sample (10 µL) was used for linear RNA amplification and labelling with Cy5 or Cy3. All reactions were performed using half of the amounts indicated by the manufacturer. Briefly, a transcription master mix was prepared (7.65 µL nuclease-free water; 10 µL 4x transcription buffer; 3 µL 0.1 M DTT; 4 µL NTP mix, 3.2 µL 50% PEG; 0.25 µL RNaseOUT; 0.3 µL inorganic pyrophosphatase; 0.4 µl T7 RNA Polymerase; 1.2 µL cyanine 3-CTP or cyanine 5-CTP, total volume 30 µL). 30 µL of transcription mastermix was added to10 µL cDNA. In vitro transcription and labelling were carried out at 40°C for 2 h. The labelled cRNA samples were purified using Qiagen Rneasy mini-spin columns (Qiagen, Venlo, The Netherlands). Dye incorporation and cRNA concentration was measured using the ‘micro-array measurement mode’ of the Nanodrop spectrophotometer (NanoDrop Technologies Wilmintog, Delaware, USA). Yield of each individual sample was >825 ng and specific activity >8.0 pmol Cy3 or Cy5 per µg cRNA. All Cy3 cRNAs were pooled to serve as a standard reference pool.

growth_protocol: Blood samples (1.5-2.5 mL) were collected from rats in feeding conditions from the safena vein, using heparine in NaCl (0.9%) as anticoagulant.

extract_protocol: Total RNA from PBMC samples was extracted using Tripure Reagent (Roche Diagnostic Barcelona, Spain) and purified with a Qiagen RNeasy Mini Kit spin columns (Izasa SA, Barcelona, Spain).

treatment_protocol: Immediately after blood collection, PBMC were isolated by Ficoll gradient separation.

tag: Wistar, Gender

value: Male, Age:6 months, Tissue:PBMC

source_name: Reference RNA.  Pool of equal molar total RNA samples of all groups analyzed.


title: Adult testes pool 2


title: PBMC_Fed_Con_4

source_name: PBMC, Fed, Control,  4


title: Larvae_Control_RepB_Block2

city: Kerrville

first: Leonel

middle: (Leo)

last: Saldivar

address: 2700 Fredericksburg Rd.

department: Agriculture

institute: USDA

hyb_protocol: done at NimbleGen Inc.

scan_protocol: The hybridized arrays were scanned with an Axon scanner (Axon Instruments, Union City, CA)

data_processing: The intensity raw values were normalized using quantile normalization to adjust intensity values which arise from variation in the technology rather than from biological differences between the RNA samples. It is important to remove as much of the non-biological variation in signal intensity as possible.  One robust way is by using a ‘complete data method’ of normalization.  The method is called ‘complete data method’ because it makes use of data from all arrays in an experiment to form the normalizing relation.  Quantile normalization is a complete data method and this is what was implemented for our dataset.  The goal of this type of normalization is to equalize the distribution of probe intensities for each array in a set of arrays.   (Bolstad, 2001)   Gene Calls: The gene calls were generated using the Robust Multichip Average (RMA) algorithm.  (Irizarray,et al., 2003A,  Irizarray, et al., 2003B,  Bolstad, 2003)   The software package tools used for normalization and gene calling are available through Bioconductor project at:  www.bioconductor.org    Further analysis was done on MeV (Microarray Experiment Viewer) after the data set was log base 2 transformed.

organism: Rhipicephalus microplus

source_name: B. microplus Larvae

label_protocol: Dye: CY3

growth_protocol: To obtain uninfected ticks, R. microplus larvae from 1.0 g of eggs were placed on a calf on day 1. On day 22 the first replete tick females were collected and they continued to drop until the animal was euthanized on day 31. Replete female ticks for this study were collected on day 22 and dissections were done 4 days post-repletion while females were actively ovipositing.  To obtain infected ticks, R. microplus larvae from 1.0 g of eggs were placed on a calf on day 1 and again 2 days later (total larvae from 2 g of eggs). The calf was artificially infected with B. bovis by inoculating it intravenously with 1.8 ml of B. bovis blood stabilate (T2Bo strain of B. bovis, made on 14 November 1989 at 5.5% parasitized erythrocytes and stored in liquid nitrogen since it was made) on day 14. The calf reached its peak level of infection as determined by rectal temperature on approximately day 22.  The first replete females were collected on day 20, and they continued to drop until the animal was euthanized on day 24. Replete female ticks for this study were collected on day 21, and dissected 9 days post-repletion, while actively ovipositing.

extract_protocol: Ovaries were dissected from engorged adult females that were either infected with B. bovis (infected ticks) or not (control ticks). Ticks were held in place for dissection with melted wax in Petri dishes and dissected under phosphatebuffered saline (PBS). The ventral cuticle was excised with a scalpel, the ovaries were removed, rinsed in sterile PBS and then held in PBS on ice in groups of five ticks per tube until they were frozen at  80 1C.   Total RNA was isolated from gut, ovary and larval material, using two consecutive 40 sec runs in the FastPrep-24 Tissue and Cell Homogenizer and Lysing Matrix D (Qbiogene, Irvine, CA). A setting of 6.0 with a 3 min ice incubation between runs was used, followed by RNA isolation with the Fast RNA Pro Green Kit (Qbiogene) and subsequent lithium chloride precipitation using the Totally RNA Kit reagents (Ambion Inc., Austin, TX).  Approximately 50 mg total RNA was treated with Turbo DNA-free kit (Ambion Inc.) in two 100 ml aliquots each treated with 2 ml of Turbo DNAse per kit protocols.  RNA integrity was verified by formaldehyde gel electrophoresis and staining in GelStar Nucleic Acid Gel Stain (Cambrex Bio Science, Rockland, ME).  DNA-free RNA was sent to NimbleGen for use in microarray analysis.

treatment_protocol: Tissues (Ovaries, gut) were dissected from engorged adult females that were either infected with B. bovis (infected ticks) or not (control ticks). Ticks were held in place for dissection with melted wax in Petri dishes and dissected under phosphatebuffered saline (PBS). The ventral cuticle was excised with a scalpel, the ovaries were removed, rinsed in sterile PBS and then held in PBS on ice in groups of five ticks per tube until they were frozen at  80 1C.   Total RNA was isolated from gut, ovary and larval material, using two consecutive 40 sec runs in the FastPrep-24 Tissue and Cell Homogenizer and Lysing Matrix D (Qbiogene, Irvine, CA). A setting of 6.0 with a 3 min ice incubation between runs was used, followed by RNA isolation with the Fast RNA Pro Green Kit (Qbiogene) and subsequent lithium chloride precipitation using the Totally RNA Kit reagents (Ambion Inc., Austin, TX).  Approximately 50 mg total RNA was treated with Turbo DNA-free kit (Ambion Inc.) in two 100 ml aliquots each treated with 2 ml of Turbo DNAse per kit protocols.  RNA integrity was verified by formaldehyde gel electrophoresis and staining in GelStar Nucleic Acid Gel Stain (Cambrex Bio Science, Rockland, ME).  DNA-free RNA was sent to NimbleGen for use in microarray analysis.

tag: R. microplus used in these studies are from the La Minita strain maintained at The University of Idaho Holm Research Center (HRC) since 1999; at the time of these studies, this colony was in approximately the 20th laboratory generation. Ticks for the colony were originally collected in Starr Co. Texas in 1996.


title: PBMC_Fed_Con_13

source_name: PBMC, Fed, Control,  13


title: Adult ovary pool 1


title: Larvae_Infected_RepA_Block1


title: PBMC_Fed_Caf_7

source_name: PBMC, Fed, Cafeteria, 7


title: PBMC_Fed_Caf_13

source_name: PBMC, Fed, Cafeteria, 13


title: Larvae_Infected_RepB_Block2


title: Larvae_Infected_RepA_Block2


title: Larvae_Control_RepA_Block2


title: Ovary_Infected_RepB_Block1

source_name: B. microplus Ovary


title: Ovary_Infected_RepB_Block2


title: Larvae_Control_RepB_Block1


title: PBMC_Fed_Caf_1

source_name: PBMC, Fed, Cafeteria, 1


title: PBMC_Fed_Caf_10

source_name: PBMC, Fed, Cafeteria, 10


title: PBMC_Fed_Con_1

source_name: PBMC, Fed, Control,  1


title: PBMC_Fed_Caf_4

source_name: PBMC, Fed, Cafeteria, 4


title: Ovary_Infected_RepA_Block2


title: Larvae_Control_RepA_Block1


title: Ovary_Infected_RepA_Block1


title: Non-Recurrent-NSCLC-15

city: Minneapolis

first: David

middle: A.

last: Potter

address: 420 Delaware St. SE

department: Division of Hematology, Oncology and Transplantation

institute: University of Minnesota

description: Gene expression data from patient with non-recurrent cancer (frozen NSCLC tumor tissue)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on HGU133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: non-recurrent NSCLC tumor

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

extract_protocol: Resected tumor tissue was placed in liquid nitrogen immediately following resection. Specimens were homogenized using a Polytron homogenizer (Brinkmann Instruments, Westbury, NY) in ice-cold Trizol reagent (Gibco BRL, Gaithersburg, MD). Trizol extraction was followed by clean-up using the Qiagen RNeasy Mini-kit.

tag: from patient with non-recurrent cancer


title: Ovary_Control_RepB_Block1


title: Ovary_Control_RepA_Block2


title: Gut_Infected_RepB_Block2

source_name: B. microplus Gut


title: Ovary_Control_RepB_Block2


title: Non-Recurrent-NSCLC-16


title: Non-Recurrent-NSCLC-14


title: Ovary_Control_RepA_Block1


title: Gut_Infected_RepB_Block1


title: Gut_Infected_RepA_Block1


title: Non-Recurrent-NSCLC-12


title: Gut_Control_RepA_Block1


title: Non-Recurrent-NSCLC-8


title: Gut_Control_RepB_Block2


title: Gut_Control_RepA_Block2


title: Non-Recurrent-NSCLC-10


title: Gut_Control_RepB_Block1


title: Non-Recurrent-NSCLC-9


title: Gut_Infected_RepA_Block2


title: Non-Recurrent-NSCLC-11


title: Recurrent-NSCLC-11

description: Gene expression data from patient with recurrent cancer (frozen NSCLC tumor tissue)

source_name: recurrent NSCLC tumor

tag: from patient with recurrent cancer


title: Non-Recurrent-NSCLC-7


title: Non-Recurrent-NSCLC-5


title: Recurrent-NSCLC-9


title: Non-Recurrent-NSCLC-3


title: Recurrent-NSCLC-10


title: Non-Recurrent-NSCLC-4


title: Non-Recurrent-NSCLC-13


title: Larvae_Infected_RepB_Block1