title: B6J12-2.vs.B6J-1_rep1_hyb2

growth_protocol: DNA was isolated using the Puregene Kit (Gentra Systems), with the following modifications: livers were flash frozen in liquid nitrogen, ground with mortar and pestle, and dounce-homogenized in 20 ml cell lysis solution. Two additional extrections were performed with phenol/chloroform/isoamyl alcohol, and chloroform/isoamyl alcohol, and DNA was precipitated with 2 volumes isopropanol and 1/10 volume sodium acetate.


title: B6J12-4.vs.B6J-1_rep1_hyb1

status: Public on Oct 28 2007

type: genomic

city: Cold Spring Harbor

first: Ira

middle: M

last: Hall

state: NY

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

hyb_protocol: Hybs were performed in 25 uL of solution consisting of 37.5% formamide, 4x SSC, and O.1% SDS.  Samples were denatured at 95° for 5 min, pre-annealed for 30 min at 37° with 1 µg of mouse COT1 DNA, applied to the microarray, and hybridized under a coverslip at 42°C for 14-18 h.  Slides were washed for 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC,  30 sec in 0.05x SSC, and dried by centrifugation.

scan_protocol: Microarrays were scanned with an Axon GenePix 4000B scanner with pixel size set to 5um. GenePix Pro 4.0 software was used for gridding and quantitation of intensities.

data_processing: Measured intensities without background subtraction were used to calculate ratios.  Data were normalized using an intensity-based lowess curve fitting algorithm similar to that described in Yang et al (Nucleic Acids Research, 30 e15, Feb 15, 2002).

molecule: genomic DNA

organism: Mus musculus

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6J inbred mouse

label_protocol: 1.5 µg of DNA from genomic representations were differentially labeled with Cy5-dCTP or Cy3-dCTP dyes using the Amersham-Pharmacia Megaprime kit. Labeled DNA was purified with Microcon columns (Millipore) with lowTE.

extract_protocol:
DNA was isolated using the Puregene Kit (Gentra Systems), with the following modifications: livers were flash frozen in liquid nitrogen, ground with mortar and pestle, and dounce-homogenized in 20 ml cell lysis solution. Two additional extrections were performed with phenol/chloroform/isoamyl alcohol, and chloroform/isoamyl alcohol, and DNA was precipitated with 2 volumes isopropanol and 1/10 volume sodium acetate.
1.5 µg of DNA was digested with the Bgl II restriction enzyme for 8-12 hrs at 37°C.  Fragments were column-purified (Qiagen Minielute kit), and universal adaptors were added to fragments by overnight ligation with T4 ligase at 16º C.  After 22 cycles of PCR amplification with the universal primer, resulting genomic representations were predominantly composed of fragments 100-1200 bp in length.  Representations were then column-purified (Qiagen PCR purification kit).

tag: DNA prep ID

tag: Strain

tag: Tissue

value: tail

tag: Age

value: 4-8 weeks

tag: Gender

value: Female

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6J inbred mouse

value: liver


title: B6J12-6.vs.B6J12-M_rep1_hyb2

value: 6-10 months

value: Male


title: B6J12-5.vs.B6J-1_rep1_hyb1


title: B6J12-5.vs.B6J-1_rep1_hyb2


title: B6J12-2.vs.B6J-1_rep1_hyb1


title: B6J12-1.vs.B6J-1_rep1_hyb1


title: B6J12-3.vs.B6J-1_rep1_hyb1


title: B6J10-7.vs.B6J10-M _rep1_hyb2


title: B6J10-6.vs.B6J10-M _rep1_hyb4


title: B6J10-4.vs.B6J10-F_rep1_hyb2


title: B6J12-1.vs.B6J-1_rep1_hyb2


title: B6J10-5.vs.B6J10-F_rep1_hyb1


title: B6J12-3.vs.B6J-1_rep1_hyb2


title: B6J10-F.vs. B6J10-M _rep1_hyb3


title: B6J10-3.vs.B6J10-F_rep1_hyb1


title: B6J10-6.vs.B6J10-M _rep1_hyb1


title: B6J10-1.vs.B6J10-F_rep1_hyb1


title: B6J10-7.vs.B6J10-F _rep1_hyb1


title: B6J10-5.vs.B6J10-F_rep1_hyb2


title: B6J10-6.vs.B6J10-M _rep1_hyb3


title: B6J10-2.vs.B6J10-F_rep1_hyb1


title: B6J10-1.vs.B6J10-F_rep1_hyb2


title: B6J10-6.vs.B6J10-M _rep1_hyb2


title: B6J10-3.vs.B6J10-F_rep1_hyb2


title: B6J12-6.vs.B6J12-M_rep1_hyb1


title: B6J10-F.vs. B6J10-M _rep1_hyb4


title: B6J10-4.vs.B6J10-F_rep1_hyb1


title: B6J10-2.vs.B6J10-F_rep1_hyb2


title: B6Crl7-8.vs.B6J-1_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/Crl inbred mouse


title: B6J10-F.vs. B6J10-M _rep1_hyb2


title: B6J10-M.vs.B6J-1 _rep1_hyb1


title: B6J10-F.vs. B6J10-M _rep1_hyb1


title: B6J10-M.vs.B6J-1 _rep1_hyb2


title: B6J10-F.vs.B6J-1 _rep1_hyb1


title: B6Crl7-8.vs.B6J-1_rep1_hyb2


title: B6Crl7-7.vs.B6J-1_rep2_hyb4


title: B6Crl7-8.vs.B6J-1_rep1_hyb1


title: B6Crl7-6.vs.B6J-1_rep2_hyb3


title: B6Crl7-6.vs.B6J-1_rep1_hyb2


title: B6Crl7-7.vs.B6J-1_rep2_hyb3


title: B6Crl7-8.vs.B6J-1_rep2_hyb3


title: B6Crl7-4.vs.B6J-1_rep2_hyb3


title: B6Crl7-5.vs.B6J-1_rep1_hyb2


title: B6Crl7-5.vs.B6J-1_rep2_hyb3


title: B6Crl7-6.vs.B6J-1_rep1_hyb1


title: B6Crl7-5.vs.B6J-1_rep2_hyb4


title: B6Crl7-5.vs.B6J-1_rep1_hyb1


title: B6Crl7-4.vs.B6J-1_rep1_hyb1


title: B6Crl7-6.vs.B6J-1_rep2_hyb4


title: B6Crl7-7.vs.B6J-1_rep1_hyb2


title: B6Crl7-7.vs.B6J-1_rep1_hyb1


title: B6Crl7-3.vs.B6J-1_rep1_hyb1


title: B6Crl7-3.vs.B6J-1_rep1_hyb2


title: B6Crl7-3.vs.B6J-1_rep2_hyb3


title: B6Crl7-3.vs.B6J-1_rep2_hyb4


title: B6Crl7-4.vs.B6J-1_rep1_hyb2


title: B6Crl7-4.vs.B6J-1_rep2_hyb4


title: B6J10-F.vs.B6J-1 _rep1_hyb2


title: B6Crl7-1.vs.B6J-1_rep2_hyb4


title: B6Crl7-2.vs.B6J-1_rep1_hyb1


title: B6Crl7-1.vs.B6J-1_rep2_hyb3


title: B6Crl7-2.vs.B6J-1_rep1_hyb2


title: B6Crl7-2.vs.B6J-1_rep2_hyb3


title: B6Crl7-M.vs.B6J-1_rep2_hyb4


title: B6Crl7-2.vs.B6J-1_rep2_hyb4


title: B6Crl7-F.vs.B6J-1_rep1_hyb1


title: B6Crl7-F.vs.B6J-1_rep2_hyb3


title: B6Crl7-1.vs.B6J-1_rep1_hyb1


title: B6Crl7-1.vs.B6J-1_rep1_hyb2


title: B6Crl6-5.vs.B6J-1_rep1_hyb1


title: B6Crl7-M.vs.B6J-1_rep2_hyb3


title: B6Crl6-5.vs.B6J-1_rep1_hyb2


title: B6Crl6-4.vs.B6J-1_rep1_hyb2


title: B6Crl7-M.vs.B6J-1_rep1_hyb2


title: B6Crl7-M.vs.B6J-1_rep1_hyb1


title: B6Crl6-4.vs.B6J-1_rep1_hyb1


title: B6Crl7-F.vs.B6J-1_rep1_hyb2


title: B6Crl6-2.vs.B6J-1_rep1_hyb1


title: B6Crl6-1.vs.B6J-1_rep1_hyb2


title: B6Crl7-F.vs.B6J-1_rep2_hyb4


title: B6Crl6-M.vs.B6J-1_rep1_hyb2


title: B6Crl6-3.vs.B6J-1_rep1_hyb1


title: B6Crl6-2.vs.B6J-1_rep1_hyb2


title: B6Crl6-1.vs.B6J-1_rep1_hyb1


title: B6Crl6-M.vs.B6J-1_rep1_hyb1


title: B6Crl6-3.vs.B6J-1_rep1_hyb2


title: B6Crl6-F.vs.B6J-1_rep1_hyb2


title: B6Crl4-7.vs.B6J-1_rep1_hyb2


title: B6Crl6-F.vs.B6J-1_rep1_hyb1


title: B6Crl4-7.vs.B6J-1_rep1_hyb1


title: B6Crl4-2.vs.B6J-1_rep1_hyb2


title: B6Crl4-4.vs.B6J-1_rep1_hyb1


title: B6Crl4-1.vs.B6J-1_rep1_hyb2


title: B6Crl4-5.vs.B6J-1_rep1_hyb2


title: B6Crl4-3.vs.B6J-1_rep1_hyb2


title: B6Crl4-5.vs.B6J-1_rep1_hyb1


title: B6Crl4-F.vs. B6Crl4-M _rep1_hyb2


title: B6Crl4-2.vs.B6J-1_rep1_hyb1


title: B6Crl3-4.vs.B6J-1_rep1_hyb2


title: B6Crl4-6.vs.B6J-1_rep1_hyb1


title: B6Crl4-M.vs.B6J-1_rep1_hyb1


title: B6Crl4-4.vs.B6J-1_rep1_hyb2


title: B6Crl3-3.vs.B6J-1_rep1_hyb1


title: B6Crl4-1.vs.B6J-1_rep1_hyb1


title: B6Crl4-6.vs.B6J-1_rep1_hyb2


title: B6Crl4-F.vs.B6J-1_rep1_hyb1


title: B6Crl3-3.vs.B6J-1_rep1_hyb2


title: B6Crl3-5.vs.B6J-1_rep1_hyb2


title: B6Crl3-5.vs.B6J-1_rep1_hyb1


title: B6Crl3-6.vs.B6J-1_rep1_hyb2


title: B6Crl4-M.vs.B6J-1_rep1_hyb2


title: B6Crl4-F.vs. B6Crl4-M _rep1_hyb1


title: B6Crl4-F.vs.B6J-1_rep1_hyb2


title: B6Crl3-6.vs.B6J-1_rep1_hyb1


title: B6Crl3-4.vs.B6J-1_rep1_hyb1


title: B6Crl4-3.vs.B6J-1_rep1_hyb1


title: B6Crl3-2.vs.B6J-1_rep1_hyb2


title: B6Crl3-2.vs.B6J-1_rep1_hyb1


title: B6Crl3-1.vs.B6J-1_rep1_hyb1


title: B6Crl3-M.vs.B6J-1_rep1_hyb1


title: SJL/J-1.vs.SJL/J-2_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a SJL/J inbred mouse

value: SJL/J


title: B6Crl3-1.vs.B6J-1_rep1_hyb2


title: B6Crl3-F.vs.B6J-1_rep1_hyb2


title: 129S1/SvImJ-1.vs.129S1/SvImJ-2_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a 129S1/SvImJ inbred mouse


title: FVB/NJ-1.vs.FVB/NJ-2_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a FVB/NJ inbred mouse

value: FVB/NJ


title: B6Crl3-F.vs.B6J-1_rep1_hyb1


title: BALB/cByJ-1.vs.BALB/cByJ-2_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a BALB/cByJ inbred mouse

value: BALB/cByJ


title: DBA/2J-1.vs.DBA/2J-2_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a DBA/2J inbred mouse


title: A/J-1.vs.A/J-2 _rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of an A/J inbred mouse

value: A/J

source_name: Bgl II genomic representation of DNA isolated from the liver of a A/J inbred mouse


title: 129S1/SvImJ-1.vs.129S1/SvImJ-2_rep1_hyb2


title: C3H/HeJ-1.vs.C3H/HeJ-2_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C3H/HeJ inbred mouse


title: BALB/cByJ-1.vs.BALB/cByJ-2_rep1_hyb2


title: B6Crl3-M.vs.B6J-1_rep1_hyb2


title: FVB/NJ-1.vs.FVB/NJ-2_rep1_hyb1


title: C58/J-1.vs.C58/J-2_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C58/J inbred mouse


title: C57L/J-1.vs.C57L/J-2_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57L/J inbred mouse


title: C57L/J-1.vs.C57L/J-2_rep1_hyb1


title: C57BL/10J-1.vs.C57BL/10J-2_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/10J inbred mouse


title: C57BR/cdJ-1.vs.C57BR/cdJ-2_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BR/cdJ inbred mouse


title: C3H/HeJ-1.vs.C3H/HeJ-2_rep1_hyb2


title: SJL/J-1.vs.SJL/J-2_rep1_hyb2


title: DBA/2J-1.vs.DBA/2J-2_rep1_hyb1


title: A/J-1.vs.A/J-2 _rep1_hyb2


title: C57BLKS/J-1.vs.C57BLKS/J-2_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BLKS/J inbred mouse


title: C57BLKS/J-1.vs.C57BLKS/J-2_rep1_hyb1


title: C58/J-1.vs.C58/J-2_rep1_hyb2


title: C57BR/cdJ-1.vs.C57BR/cdJ-2_rep1_hyb2


title: C57BL/10J-1.vs.C57BL/10J-2_rep1_hyb1


title: B6J-L.vs.B6J-1-L_rep1_hyb1

value: 7 months


title: B6J-L.vs.B6J-1-L_rep1_hyb2


title: B6J-T.vs.B6J-1-T_rep1_hyb1


title: B6J-1.vs.B6J-2_rep2_hyb4


title: B6J-1.vs.B6J-2_rep1_hyb2


title: B6J-1.vs.B6J-2_rep2_hyb3


title: BALB/cByJ.vs.C3H/HeJ_rep1_hyb1


title: B6ByJ.vs.C57BR/cdJ_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6ByJ inbred mouse


title: DBA/2J.vs.A/J  _rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a  A/J inbred mouse


title: DBA/2J.vs.A/J  _rep2_hyb4


title: BALB/cByJ.vs.C3H/HeJ_rep2_hyb4


title: BALB/cByJ.vs.DBA/2J_rep1_hyb2


title: B6ByJ.vs.C57BR/cdJ_rep1_hyb1


title: BALB/cByJ.vs.DBA/2J_rep2_hyb4


title: B6Icr.vs.B6N_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6N inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6Icr inbred mouse


title: DBA/2J.vs.A/J  _rep2_hyb3


title: B6NSim.vs.B6NTac_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6NTac inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the liver of a  C57BL/6NSim inbred mouse


title: B6NSim.vs.B6N_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6NSim inbred mouse


title: B6J-1.vs.B6J-2_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6J inbred mouse


title: B6Icr.vs.B6N_rep1_hyb1


title: BALB/cByJ.vs.DBA/2J_rep2_hyb3

source_name: Bgl II genomic representation of DNA isolated from the liver of a BALB/cByJ inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the liver of a DBA/2J inbred mouse


title: DBA/2J.vs.A/J  _rep1_hyb1


title: BALB/cByJ.vs.C3H/HeJ_rep1_hyb2


title: B6NSim.vs.B6NTac_rep1_hyb1


title: BALB/cByJ.vs.DBA/2J_rep1_hyb1


title: B6J-T.vs.B6J-1-T_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6J inbred mouse


title: BALB/cByJ.vs.C3H/HeJ_rep2_hyb3

source_name: Bgl II genomic representation of DNA isolated from the liver of a C3H/HeJ inbred mouse


title: B6NSim.vs.B6N_rep2_hyb3

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6NSim inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6N inbred mouse


title: B6NSim.vs.B6N_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the tail of a  C57BL/6NSim inbred mouse


title: B6NTac.vs.B6NTacAce_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a  C57BL/6NTac inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6NTacAce inbred mouse


title: B6NTac.vs.B6N_rep2_hyb4


title: B6NSim.vs.B6N_rep1_hyb1


title: B6NTac.vs.B6N_rep2_hyb3


title: B6NTac.vs.B6NTacAce_rep1_hyb2


title: SJL/J.vs.B6J_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the liver of a SJL/J inbred mouse


title: B6OlaHsdF.vs.B6OlaHsdG_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6OlaHsdF inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6OlaHsdG inbred mouse


title: B6HanZtm.vs.B6BomTac_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6HanZtm inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the liver of a  C57BL/6BomTac inbred mouse


title: FVB/NJ.vs.B6J_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the liver of a FVB/NJ inbred mouse


title: SJL/J.vs.B6J_rep3_hyb5


title: B6EiJ.vs.B6BomTac_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6EiJ inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6BomTac inbred mouse


title: 129S1/SvImJ.vs.B6J_rep2_hyb3

source_name: Bgl II genomic representation of DNA isolated from the liver of a 129S1/SvImJ inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6J inbred mouse


title: SJL/J.vs.B6J_rep1_hyb1


title: B6HanZtm.vs.B6BomTac_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6OlaHsdC inbred mouse


title: 129S1/SvImJ.vs.B6J_rep2_hyb4


title: B6NTac.vs.B6N_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6NTac inbred mouse


title: SJL/J.vs.B6J_rep3_hyb6


title: SJL/J.vs.B6J_rep1_hyb2


title: B6OlaHsdC.vs.B6BomTac_rep1_hyb2


title: FVB/NJ.vs.B6J_rep1_hyb1


title: FVB/NJ.vs.B6J_rep1_hyb2


title: 129S1/SvImJ.vs.B6J_rep1_hyb2


title: B6OlaHsdF.vs.B6OlaHsdG_rep1_hyb2


title: 129S1/SvImJ.vs.B6J_rep1_hyb1


title: B6OlaHsdC.vs.B6BomTac_rep1_hyb1


title: SJL/J.vs.B6J_rep2_hyb3


title: BALB/cByJ.vs.B6J_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the liver of a BALB/cByJ inbred mouse


title: B6EiJ.vs.B6BomTac_rep1_hyb2


title: FVB/NJ.vs.B6J_rep2_hyb3


title: BALB/cByJ.vs.B6J_rep1_hyb1


title: BALB/cByJ.vs.B6J_rep2_hyb3


title: DBA/2J.vs.B6J_rep3_hyb6

source_name: Bgl II genomic representation of DNA isolated from the liver of a DBA/2J inbred mouse


title: DBA/2J.vs.B6J_rep1_hyb2


title: B6NTac.vs.B6N_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6N inbred mouse


title: DBA/2J.vs.B6J_rep2_hyb3


title: C3H/HeJ.vs.B6J_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C3H/HeJ inbred mouse


title: DBA/2J.vs.B6J_rep3_hyb5


title: A/J.vs.B6J_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a A/J inbred mouse


title: C3H/HeJ.vs.B6J_rep2_hyb3


title: DBA/2J.vs.B6J_rep2_hyb4


title: C3H/HeJ.vs.B6J_rep1_hyb2


title: A/J.vs.B6J_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of an A/J inbred mouse


title: C58/J.vs.B6J_rep2_hyb3

source_name: Bgl II genomic representation of DNA isolated from the liver of a C58/J inbred mouse


title: A/J.vs.B6J_rep2_hyb3


title: BALB/cByJ.vs.B6J_rep1_hyb2


title: C58/J.vs.B6J_rep2_hyb4


title: A/J.vs.B6J_rep2_hyb4


title: C3H/HeJ.vs.B6J_rep2_hyb4


title: DBA/2J.vs.B6J_rep1_hyb1


title: C57BLKS/J.vs.B6J_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BLKS/J inbred mouse


title: C57BLKS/J.vs.B6J_rep2_hyb3


title: C57BLKS/J.vs.B6J_rep1_hyb1


title: C58/J.vs.B6J_rep1_hyb1


title: C57L/J.vs.B6J_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57L/J inbred mouse


title: C57L/J.vs.B6J_rep2_hyb4


title: C57BR/cdJ.vs.B6J_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BR/cdJ inbred mouse


title: C57BLKS/J.vs.B6J_rep1_hyb2


title: C57BR/cdJ.vs.B6J_rep2_hyb3


title: C57L/J.vs.B6J_rep1_hyb1


title: C57L/J.vs.B6J_rep2_hyb3


title: C57BR/cdJ.vs.B6J_rep1_hyb1


title: C58/J.vs.B6J_rep1_hyb2


title: C57BL/10J.vs.B6J_rep2_hyb3

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/10J inbred mouse


title: C57BL/10J.vs.B6J_rep3_hyb6


title: B6EiJ.vs.B6J_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6J inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6EiJ inbred mouse


title: B6EiJ.vs.B6J_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6EiJ inbred mouse


title: C57BL/10J.vs.B6J_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6J inbred mouse


title: C57BL/10J.vs.B6J_rep2_hyb4


title: C57BL/10J.vs.B6J_rep3_hyb5


title: B6EiJ.vs.B6J_rep1_hyb1


title: B6OlaHsdC.vs.B6J_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6OlaHsdC inbred mouse


title: B6EiJ.vs.B6J_rep3_hyb5


title: B6OlaHsdC.vs.B6J_rep2_hyb3


title: B6EiJ.vs.B6J_rep2_hyb3


title: B6OlaHsdC.vs.B6J_rep3_hyb6


title: B6OlaHsdC.vs.B6J_rep3_hyb5


title: B6OlaHsdC.vs.B6J_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6OlaHsdC inbred mouse


title: B6OlaHsdF.vs.B6J_rep3_hyb6

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6OlaHsdF inbred mouse


title: B6EiJ.vs.B6J_rep3_hyb6


title: C57BL/10J.vs.B6J_rep1_hyb2


title: B6OlaHsdC.vs.B6J_rep1_hyb1


title: B6OlaHsdF.vs.B6J_rep3_hyb5


title: B6OlaHsdF.vs.B6J_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6OlaHsdF inbred mouse


title: B6OlaHsdF.vs.B6J_rep2_hyb3


title: B6OlaHsdG.vs.B6J_rep3_hyb5

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6OlaHsdG inbred mouse


title: C57BR/cdJ.vs.B6J_rep1_hyb2


title: B6OlaHsdF.vs.B6J_rep1_hyb1


title: B6OlaHsdG.vs.B6J_rep3_hyb6


title: B6OlaHsdG.vs.B6J_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6OlaHsdG inbred mouse


title: B6OlaHsdG.vs.B6J_rep2_hyb4


title: B6OlaHsdF.vs.B6J_rep1_hyb2


title: B6HanZtm.vs.B6J_rep3_hyb5

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6HanZtm inbred mouse


title: B6OlaHsdG.vs.B6J_rep1_hyb1


title: B6HanZtm.vs.B6J_rep3_hyb6


title: B6OlaHsdG.vs.B6J_rep2_hyb3


title: B6HanZtm.vs.B6J_rep2_hyb4


title: B6Crl4-6.vs.B6J_hyb3

hyb_protocol: Hybs were performed in 25 uL of solution consisting of 37.5% formamide, 4x SSC, and O.1% SDS.  Samples were denatured at 95° for 5 min, pre-annealed for 30 min at 37° with 1 µg of mouse COT1 DNA, applied to the microarray, and hybridized under a coverslip at 42°C for 14-18 h.  Slides were washed for 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC,  30 sec in 0.05x SSC.

data_processing: Data were normalized using an intensity-based lowess curve fitting algorithm similar to that described in Yang et al (Nucleic Acids Research, 30 e15, Feb 15, 2002).

source_name: Genomic DNA isolated from the tail of a C57BL/6J inbred mouse

label_protocol: 2 µg of DNA was sonicated to a size range of 200-2000 bp and labeled with Cy5-dCTP or Cy3-dCTP dyes using the Amersham-Pharmacia Megaprime kit.  Labeled DNA was purified with Microcon columns (Millipore) with lowTE.

growth_protocol: Wild-type mice were maintained on a standard laboratory diet

extract_protocol: DNA was isolated using the Puregene Kit (Gentra Systems), with the following modifications: livers were flash frozen in liquid nitrogen, ground with mortar and pestle, and dounce-homogenized in 20 ml cell lysis solution. Two additional extrections were performed with phenol/chloroform/isoamyl alcohol, and chloroform/isoamyl alcohol, and DNA was precipitated with 2 volumes isopropanol and 1/10 volume sodium acetate.

source_name: Genomic DNA isolated from the tail of a C57BL/6Crl inbred mouse


title: B6Crl7-F.vs.B6J_hyb2


title: B6Crl7-F.vs.B6J_hyb3


title: B6HanZtm.vs.B6J_rep2_hyb3


title: B6Crl4-6.vs.B6J_hyb1


title: B6HanZtm.vs.B6J_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6HanZtm inbred mouse


title: B6Crl4-M.vs.B6J_hyb2


title: B6BomTac.vs.B6J_rep4_hyb8

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6BomTac inbred mouse


title: B6Crl7-F.vs.B6J_hyb1


title: B6BomTac.vs.B6J_rep3_hyb6


title: B6BomTac.vs.B6J_rep3_hyb5

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6BomTac inbred mouse


title: B6BomTac.vs.B6J_rep4_hyb7


title: B6BomTac.vs.B6J_rep2_hyb4


title: B6Crl4-6.vs.B6J_hyb2


title: B6BomTac.vs.B6J_rep2_hyb3


title: SJL/J-1.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C57BL/6J inbred mouse

source_name: Genomic DNA isolated from the liver of a SJL/J inbred mouse


title: B6Crl4-M.vs.B6J_hyb3


title: B6Crl4-F.vs.B6J_hyb1


title: B6Crl4-F.vs.B6J_hyb2


title: B6HanZtm.vs.B6J_rep1_hyb1


title: FVB/NJ-1.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a FVB/NJ inbred mouse


title: FVB/NJ-1.vs.B6J_hyb3


title: B6BomTac.vs.B6J_rep1_hyb2


title: B6BomTac.vs.B6J_rep1_hyb1


title: B6Crl4-F.vs.B6J_hyb3


title: SJL/J-1.vs.B6J_hyb3


title: B6N.vs.B6J_rep3_hyb6

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6J inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6N(e84) inbred mouse


title: B6Crl4-M.vs.B6J_hyb1


title: B6N.vs.B6J_rep3_hyb5


title: 129S1/SvImJ-1.vs.B6J_hyb3

source_name: Genomic DNA isolated from the liver of a 129S1/SvImJ inbred mouse


title: 129S1/SvImJ-1.vs.B6J_hyb2


title: B6N.vs.B6J_rep2_hyb4


title: FVB/NJ-1.vs.B6J_hyb1


title: B6NSim.vs.B6J_rep3_hyb6

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/NSim inbred mouse


title: B6N.vs.B6J_rep2_hyb3


title: 129S1/SvImJ-1.vs.B6J_hyb1


title: B6N.vs.B6J_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6N(e84) inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6J inbred mouse


title: SJL/J-1.vs.B6J_hyb1


title: B6N.vs.B6J_rep1_hyb2


title: B6NSim.vs.B6J_rep3_hyb5


title: A/J-1.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of an A/J inbred mouse


title: B6NSim.vs.B6J_rep2_hyb4


title: B6NSim.vs.B6J_rep2_hyb3


title: A/J-1.vs.B6J_hyb1


title: BALB/cByJ-1.vs.B6J_hyb2

hyb_protocol: Hybridizations were carried out for 18 hr at 42°C using the Maui Hybridization System (BioMicro Systems). Arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) .

data_processing: Signal intensities were normalized using the normalize.qspline method from the affy Bioconductor package.

label_protocol: 1 ug of DNA was sonicated to a size range of 500-2000 bp, denatured at 98°C with Cy3 or Cy5 labeled random nonamer (TriLink Biotechnologies), chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each, Invitrogen) for 2 hr at 37°C.  End products were precipitated with isopropanol and resuspended in water.

source_name: Genomic DNA isolated from the liver of a BALB/cByJ inbred mouse


title: BALB/cByJ-1.vs.B6J_hyb1


title: A/J-1.vs.B6J_hyb3


title: B6NTacAce.vs.B6J_rep3_hyb6

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6NTacAce  inbred mouse


title: B6NSim.vs.B6J_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/NSim inbred mouse


title: B6NTacAce.vs.B6J_rep3_hyb5


title: DBA/2J-1.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a DBA/2J inbred mouse


title: B6NTacAce.vs.B6J_rep2_hyb4


title: C3H/HeJ-1.vs.B6J_hyb3

source_name: Genomic DNA isolated from the liver of a C3H/HeJ inbred mouse


title: C58/J-1.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C58/J inbred mouse


title: B6NSim.vs.B6J_rep1_hyb2


title: C57L/J-1.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57L/J inbred mouse


title: C58/J-1.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57BL/6J inbred mouse


title: C3H/HeJ-1.vs.B6J_hyb1


title: C57BLKS/J-1.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57BLKS/J inbred mouse


title: DBA/2J-1.vs.B6J_hyb2


title: B6NTacAce.vs.B6J_rep2_hyb3


title: C57BL/10J-1.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C57BL/10J inbred mouse


title: C57L/J-1.vs.B6J_hyb2


title: B6NTac.vs.B6J_rep2_hyb3

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6NTac  inbred mouse


title: C57BLKS/J-1.vs.B6J_hyb2


title: B6NTac.vs.B6J_rep3_hyb5

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6NTac  inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the ltail of a C57BL/6J inbred mouse


title: C57BR/cdJ-1.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C57BR/cdJ inbred mouse


title: C3H/HeJ-1.vs.B6J_hyb2


title: B6NTacAce.vs.B6J_rep1_hyb1


title: B6NTac.vs.B6J_rep3_hyb6


title: B6NTac.vs.B6J_rep2_hyb4


title: B6NTac.vs.B6J_rep1_hyb2


title: B6EiJ.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C57BL/6EiJ inbred mouse


title: B6NTac.vs.B6J_rep1_hyb1

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6J inbred mouse


title: B6NTacAce.vs.B6J_rep1_hyb2


title: B6Icr.vs.B6J_rep4_hyb10

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6J inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6Icr inbred mouse


title: B6Icr.vs.B6J_rep4_hyb9


title: C57BR/cdJ-1.vs.B6J_hyb1


title: B6OlaHsdF.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57BL/6OlaHsdF inbred mouse


title: B6EiJ.vs.B6J_hyb1


title: B6Icr.vs.B6J_rep4_hyb8


title: B6Icr.vs.B6J_rep3_hyb5


title: B6Icr.vs.B6J_rep3_hyb6


title: B6OlaHsdF.vs.B6J_hyb2


title: C57BL/10J-1.vs.B6J_hyb1


title: B6OlaHsdG.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57BL/6OlaHsdG inbred mouse


title: B6Icr.vs.B6J_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6Icr inbred mouse


title: B6HanZtm.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C57BL/6HanZtm inbred mouse


title: B6Icr.vs.B6J_rep2_hyb3


title: B6Icr.vs.B6J_rep1_hyb2


title: B6ByJ.vs.B6J_rep3_hyb5

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6ByJ inbred mouse


title: B6OlaHsdC.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C57BL/6OlaHsdC inbred mouse


title: B6Icr.vs.B6J_rep1_hyb1


title: B6Icr.vs.B6J_rep4_hyb7


title: B6OlaHsdC.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57BL/6J inbred mouse


title: B6ByJ.vs.B6J_rep3_hyb6


title: B6ByJ.vs.B6J_rep2_hyb4

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6ByJ inbred mouse


title: B6HanZtm.vs.B6J_hyb1


title: B6ByJ.vs.B6J_rep2_hyb3


title: B6BomTac.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C57BL/6BomTac inbred mouse


title: H3K4me3 on chromosome 2L - replicate 2

status: Public on Oct 27 2007

city: Basel

first: Oliver

last: Bell

address: Maulbeerstr. 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

description: according to Weber et al. Nature Genetics 2005

hyb_protocol: Labeled DNA was co-hybridized to a chromosomal tiling array representing chromosome 2L of the Drosophila genome in a 2kb tiling resolution as described (Macalpine et al., 2004). Two repeats (including dye swap) starting from independent ChIP experiments were carried out.

scan_protocol: After hybridization and washing, slides were scanned (Axon).

data_processing: Fluorescent reads were analyzed according to standard normalization and filtering criteria in the GenePix software package (Axon).

organism: Drosophila melanogaster

source_name: DNA bound by H3K4me3-specific antibody

label_protocol: Input and antibody-bound DNA were separately amplified and labeled as described (Schübeler et al. 2004) except using indirect labeling via aminoallyl-modified nucleotides.

extract_protocol: protocol according to Wirbelauer et al. 2005

tag: immunoprecipitated DNA from sonicated chromatin prepared from female Drosophila Kc cells

source_name: input DNA

tag: genomic DNA from sonicated chromatin prepared from female Drosophila Kc cells


title: B6ByJ.vs.B6J_rep1_hyb2


title: B6NSim.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57BL/6NSim inbred mouse


title: H3K36me3 on chromosome 2L - replicate 2

source_name: DNA bound by H3K36me3-specific antibody


title: B6ByJ.vs.B6J_rep1_hyb1


title: B6N.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C57BL/N inbred mouse


title: B6NTacAce v B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57BL/6NTacAce inbred mouse


title: B6OlaHsdG.vs.B6J_hyb2


title: B6N.vs.B6J_hyb1


title: B6NSim.vs.B6J_hyb2


title: not1-2_spt3_rep1

status: Public on Oct 26 2007

type: RNA

city: Geneva

first: Martine

last: Collart

address: Rue Michel-Servet 1, Centre Médical Universitaire

department: Microbiology and Molecular Medicine

institute: University of Geneva

hyb_protocol: standard Affymetrix procedure

scan_protocol: scan analyzed by Affymetrix' MicroArraySuite, MicroDB and DataMiningTool

data_processing: Signal intensities from CHP using ArrayAssist v2.6. Significance level set to P=0.05. Only mRNAs expressed at similar levels in the duplicate samples which were also signicantly different in the other strains were analyzed.

label: biotin

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: not1-2 spt3 strain

label_protocol: standard Affymetrix procedure

growth_protocol: Cells were grown for 24 hr at 30°C in liquid glucose-rich medium and then transferred at an OD600 of 0.2 to 37.5°C (restrictive temperature). RNA was extracted when the cells were at an OD600 of 0.8.

extract_protocol: acid phenol method

tag: MATα ura3-52 trp1 leu2Δ::PET56 gcn4 gal2 not1-2 spt3::TRP1


title: not1-2_spt3_rep2


title: H3K36me2 on chromosome 2L - replicate 1

source_name: cy5 input DNA

source_name: DNA bound by H3K36me2-specific antibody


title: H3K36me2 on chromosome 2L - replicate 2

source_name: DNA bound with H3K36me2-specific antibody


title: spt3_rep2

source_name: spt3 strain

tag: MATα ura3-52 trp1 leu2Δ::PET56 gcn4 gal2 spt3::TRP1


title: B6NTac.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C57BL/NTac inbred mouse


title: Liver cancer compared with nontumor tissues developed in AID Tg mouse

city: Kyoto

first: Toshiyuki

last: Morisawa

address: 54 Kawahara-cho,Shogoin

department: Gastroenterology and Hepatology

country: Japan

institute: Kyoto University

description: no additional information

hyb_protocol: Hybridizations to the microarray were performed using the In situ Hybridization Kit Plus (Agilent). Doses of 750 ng cyanine 3-labeled cRNA, 750 ng cyanine 5-labeled cRNA, and control targets were mixed and fragmented in the kit’s fragmentation buffer, and then hybridized to the microarrays for 17 hours at 60°C in a hybridization rotator (Agilent) set to rotate at 4 rpm. Microarrays were washed in 6×SSC with 0.005% Triton X-102 at RT for 10 min, followed by 0.1×SSC with 0.005% Triton X-102 at 4°C for 5 min.

scan_protocol: The slides were dried, and then scanned by the Agilent G2565B Microarray Scanner System.

data_processing:
Data were analyzed using the Agilent Feature Extraction Software version 8.5.1.1.
A rank consistency filter and LOWESS were used for dye normalization.

molecule: total RNA

source_name: liver cancer tissue in AID Tg mouse

label_protocol: The RNA was amplified and labeled by the Low RNA Input Fluorescent Linear Amplification Kit (Agilent). To synthesize cDNA, 500 ng total RNA was used. Sample were labeled by cyanine 3 (PerkinElmer Life Sciences, Inc., Boston, MA)

extract_protocol: Total RNA was extracted from tissues using RNA assay Mini Kit(Qiagen).

tag: Strain:B2 line(AID Tg mouse)

tag: Age:52 weeks

tag: Tissues:liver cancer

label_protocol: The RNA was amplified and labeled by the Low RNA Input Fluorescent Linear Amplification Kit (Agilent). To synthesize cDNA, 500 ng total RNA was used. Sample were labeled by cyanine 5 (PerkinElmer Life Sciences, Inc., Boston, MA)

tag: Tissues:nontumor liver tissue in the AID Tg mouse developed the liver cancer


title: Gastric cancer compared with nontumor tissue developed in AID Tg mouse

description: no additional information

source_name: gastric cancer tissue in AID Tg mouse

extract_protocol: Total RNA was extracted from tissues using RNA assay Mini Kit (Qiagen).

tag: Tissues:gastric cancer

tag: Tissues:nontumor gastric tissue in the AID Tg mouse developed the gastric cancer


title: B6NTac.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57BL/6J inbred mouse


title: H3K36me3 on chromosome 2L - replicate 1

source_name: DNA bound with H3K36me3-specific antibody


title: H3K4me3 on chromosome 2L - replicate 1

scan_protocol: After hybridization and washing slides, were scanned (Axon).


title: Lung cancer developed in AID Tg mouse compared with normal lung in Wt mouse

description: no additional information

source_name: lung cancer tissue in AID Tg mouse

tag: Age:76 weeks

tag: Tissues:lung cancer

source_name: normal lung tissue in Wt mouse

tag: Age:78 weeks

tag: Tissues:normal lung tissue


title: spt3_rep1


title: B6NTacAce v B6J_hyb2

tag: DNA prep ID

tag: Strain

tag: Tissue


title: B6Crl.vs.B6J_hyb2

source_name: Genomic DNA isolated from the tail of a C57BL/6Crl inbred mouse

tag: Age

tag: Gender

source_name: Genomic DNA isolated from the tail of a C57BL/6J inbred mouse


title: not1-2_rep1

source_name: not1-2 strain

tag: MATα ura3-52 trp1 leu2Δ::PET56 gcn4 gal2 not1-2


title: wildtype_rep1

source_name: wild type strain

tag: MATa ura3-52 trp1 leu2Δ::PET56 gcn4 gal2


title: B6BomTac.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57BL/6BomTac inbred mouse


title: wildtype_rep2


title: B6Crl.vs.B6J_hyb3


title: B6ByJ.vs.B6J_hyb2

source_name: Genomic DNA isolated from the liver of a C57BL/6ByJ inbred mouse


title: not1-2_rep2


title: B6ByJ.vs.B6J_hyb1


title: B6Icr.vs.B6J_hyb1

source_name: Genomic DNA isolated from the liver of a C57BL/6Icr inbred mouse


title: LA_1

status: Public on Oct 25 2007

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

description: RNA integrity tested with Bioanalyzer (Agilent)

hyb_protocol: Affymetrix Protocol

scan_protocol: Affymetrix Protocol

data_processing: RMA transformed, log2 signal values mean centered with mean=0 and stdv=1

label: Biotin

source_name: Whole skin tissue

label_protocol: Affymetrix Protocol

extract_protocol: Mouse skin tissue, obtained 30 days after birth, was preserved in RNAlater (Ambion), and disrupted and homogenized using Mixer Mill MM301 (Retsch). Total RNA was extracted and purified from 30 mg of skin using RNeasy Fibrous Tissue Mini kit (Qiagen) following manufacturers' recommendations.

value: 30 days.

value: C57BL/DBA/FVB mixed


title: B6Crl.vs.B6J_hyb1


title: B6Icr.vs.B6J_hyb2


title: PIWI-associated piRNA in Drosophila melanogaster ovary (454 Pyrosequencing, 2006)

type: other

city: New Haven

first: Hang

last: Yin

state: CT

address: 10 Amistead Street, Room 220

department: Department of Cell Biology

institute: Yale University Stem Cell Center

description: Small RNA cDNA library was prepared according to standard small RNA cloning procedures (Pfeffer S. et al. 2005; Nat. Methods).

data_processing: Small RNA cDNA library was sequenced by 454 Life Sciences (Bradford, CT 06405). Small RNA sequences were extracted as the sequence flanked by two cloning linkers by a Perl script.

molecule: other

source_name: Lin laboratory, Yale University Stem Cell Center

extract_protocol:
RNAs were isolated from Piwi complex by immunocoprecipitation.
Small RNAs were separated on a 15% denaturing PAGE and eluted.

tag: Piwi-associated small RNAs (18~32nt) isolated from ovary extracts.

tag: Expression values indicate the cloning frequency.


title: LA_2


title: Slide 750. WT (Cy5) and Pax5-/- (Cy3).

city: Parkville

first: Stephen

middle: L

last: Nutt

state: Vic

address: 1G Royal Pde

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Cy3 dye was excited using a 532nm laser and Cy5 excited with a 635nm laser.

hyb_protocol: Microarrays were hybridized for 16 hours at 42°C with each of the fluorescently labeled probes in 25% formamide, 5X SSC, 0.1% SDS, 5μg/ml Cot-1 DNA (Invitrogen), 10mg/ml PolyA (Sigma-Aldrich) and 10mg/ml salmon sperm DNA (Sigma-Aldrich). Slides were washed at room temperature with 1X SSC/0.2% SDS, then 0.1X SSC/0.2% followed by 2 stringent washes (0.1X SSC).

scan_protocol: Slides were scanned using GenePix 4000B dual laser scanner (http://www.moleculardevices.com/pages/instruments/gn_genepix4000.html).

data_processing: The scanned microarray images were quantified using SPOT image analysis software (http://www.hca-vision.com). Statistical analysis of the microarray data used the Bioconductor software package limma (http://www.bioconductor.org). Expression values were print-tip loess normalized, with spot quality weights used to downweight spots with unusually small or large scanned sizes (Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-273.).

label_protocol: mRNA (4μg) was reverse-transcribed using Superscript II (Invitrogen) according to instructions from the manufacturer. cDNA was labeled using a protocol available on the Brown laboratory homepage. (http://cmgm.stanford.edu/pbrown/protocols/aadUTPCouplingProcedure.htm)

extract_protocol: Total RNA was isolated from from 10^8 cells using the TRIzol reagent (Invitrogen). mRNA was isolated using the Oligotex mRNA isolation kit (Qiagen) as per the manufacturers instructions.

tag: An established wild type C57BL/6 pro-B cell line (SB+/+) was expanded in the presence of IL-7 and the stromal cell line ST-2 for 7 days as described (Nutt et al Genes Dev 11:476-491 (1997).

tag: An established Pax5-/- C57BL/6 pro-B cell line (W2) was expanded in the presence of IL-7 and the stromal cell line ST-2 for 7 days as described (Nutt et al Genes Dev 11:476-491 (1997).


title: L84_2


title: Salmonella Typhimurium LT2 aroD strain replicate 3.

status: Public on Oct 24 2007

city: Brno

first: Magdalena

last: Crhanova

address: Hudcova 70

department: Bacteriology

country: Czech Republic

institute: Veterinary research institute

description: Biological replicate 3 of 3.

hyb_protocol: Hybridisation and posthybridisation washes were performed using Nexterion Slide 70mer Kit exactly according to the instructions of the manufacturer.

scan_protocol: Scanned on an ScanArray® Express scanner (PerkinElmer).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. PerkinElmer ScanArray® Express software was used.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Total RNA from Salmonella Typhimurium LT2 wt strain cells labeled with Cyanine-3 (green).

label_protocol: Approx. 5 µg of total RNA was reverse transcribed and labeled with Cyanine-3- or Cyanine-5-CTPs using LabelStarTM Array Kit (Qiagen) according to the protocol

growth_protocol: Both bacterial strains were grown for 18 hours in 20 ml Luria Broth (LB) at 37°C without shaking. Cultures were centrifuged and used for RNA purification.

extract_protocol: Total RNA was extracted using RNeasy® Mini Kit (Qiagen) following manufacturer's instructions

value: wild type strain

source_name: Total RNA from Salmonella Typhimurium LT2 aroD mutant strain cells labeled with Cyanine-5 (red).

value: aroD mutant


title: L84_1


title: Salmonella Typhimurium LT2 wt strain replicate 2.

description: Biological replicate 2 of 3.

source_name: Total RNA from Salmonella Typhimurium LT2 aroD mutant strain cells labeled with Cyanine-3 (green).

source_name: Total RNA from Salmonella Typhimurium LT2 wt strain cells labeled with Cyanine-5 (red).


title: Salmonella Typhimurium LT2 aroD strain replicate 1.

description: Biological replicate 1 of 3.


title: Salmonella Typhimurium LT2 aroD strain replicate 2.

description: Biological replicate 2 of 3.


title: L60_2


title: Salmonella Typhimurium LT2 wt strain replicate 1.

description: Biological replicate 1 of 3.


title: L60_1


title: Slide 740. IL-7 (Cy5) and Rag1-/- (Cy3).

description: Slides were scanned using GenePix 4000B dual laser scanner (http://www.moleculardevices.com/pages/instruments/gn_genepix4000.html).

data_processing:
The scanned microarray images were quantified using SPOT image
analysis software (http://www.hca-vision.com). Statistical analysis of the microarray data used the Bioconductor software package limma (http://www.bioconductor.org). Expression values were print-tip loess normalized, with spot quality weights used to downweight spots with unusually small or large scanned sizes (Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods
31:265-273.).

extract_protocol: Total RNA was isolated from from 108 cells using the TRIzol reagent (Invitrogen). mRNA was isolated using the Oligotex mRNA isolation kit (Qiagen) as per the manufacturers instructions.

tag: An established wild type C57BL/6 pro-B cell line (SB+/+) was expanded in the presence of IL-7 (2% supernatant) and the stromal cell line ST-2 for 7 days as described (Nutt et al Genes Dev 11:476-491 (1997). Cells were washed 3 times in media alone and cultured for 4 hours in the absence of IL-7.

tag: An established Rag1-/- C57BL/6 pro-B cell line was expanded in the presence of IL-7 (2% supernatant) and the stromal cell line ST-2 for 7 days as described (Nutt et al Genes Dev 11:476-491 (1997).


title: LC_3


title: LC_1

value: 30 days

value: skin


title: LC_2


title: Salmonella Typhimurium LT2 wt strain replicate 3.

description: Biological replicate 3 of 3.


title: Slide 751. Pax5 -/- (Cy5) and WT (Cy3).

tag: An established Pax5-/- C57BL/6 pro-B cell line (W2) was expanded in the presence of IL-7 (2% supernatant) and the stromal cell line ST-2 for 7 days as described (Nutt et al Genes Dev 11:476-491 (1997).

tag: An established wild type C57BL/6 pro-B cell line (SB+/+) was expanded in the presence of IL-7 (2% supernatant) and the stromal cell line ST-2 for 7 days as described (Nutt et al Genes Dev 11:476-491 (1997).


title: Slide 702. Pax5 -/- (Cy5) and Rag1 -/- (Cy3).

tag: An established rag1-/- C57BL/6 pro-B cell line was expanded in the presence of IL-7 and the stromal cell line ST-2 for 7 days as described (Nutt et al Genes Dev 11:476-491 (1997).


title: Slide 703. Rag1-/- (Cy5) and Pax5-/- (Cy3).

tag: An established Rag1-/- C57BL/6 pro-B cell line was expanded in the presence of IL-7 and the stromal cell line ST-2 for 7 days as described (Nutt et al Genes Dev 11:476-491 (1997).


title: Control subject 8

city: Clayton

first: Nigel

middle: Keith

last: Stepto

state: VIC

address: Wellington Road

department: Physiology

institute: Monash University

description: No additional information required

hyb_protocol: Both labelled sample and reference RNA were added to a new column, Cy3 (reference) then Cy5 (sample). This column was washed with PE buffer, and the pooled DNA eluted with 60µL H2O.  The solution was dried in a heated vacuum, then the pellet resuspended and mixed in 16.2 µL of H2O, 30 µL of fresh 2x Hybridization buffer (500µL formamide, 500 µL 10 X standard saline citrate [SSC] and 20µL of 10% sodium dodecyl sulphate [SDS]), 5 µL of Cot1 DNA (Invitrogen), 3.8 µL PolyA (10mg/mL; Sigma) and 5 µL Salmon Sperm DNA (10mg/mL; Invitrogen). The samples were heated to 100oC for 2min, and cooled to room temperature, before the 60µL of solution were applied to the glass micro-array slide and cover slip via capillary action.

scan_protocol: The micro-array slides were scanned using a Molecular Dynamics GenePix 4000B UV laser micro-array scanner (Amersham Pharmacia Biotech, Piscataway, NJ) interfaced with a personal computer utilising GenePix v 5.2 (Amersham Pharmacia Biotech, Piscataway, NJ)

data_processing: Data were imported into Gene Spring (Silicon Genetics, USA) version 7.1 and unless otherwise indicated statistical analysis was performed using default settings in this software. Per chip-intensity-dependent normalization (LOWESS) was carried out for each array and a group of 5962 genes were identified that satisfied the criteria of a mean signal intensity of at least 150 in at least 50% of the hybridizations. Parametric analysis of variance (Welsh ANOVA) was performed on log-transformed ratios of the normalized data for these 5962 genes with Benjamini–Hochberg false discovery rate correction at P  0.05, to identify differentially expressed genes across three populations of athletes.

organism: Homo sapiens

source_name: Human vastus lateralis, rested, healthy control

label_protocol:
RNA were prepared for labelling using the Superscript™ III indirect labelling system (Invitrogen Life Technologies, Australia) where the aRNA was mixed with 1µl spike RNA, 2µl anchored oligo (dT)20 primer (2.5mg/ml) in a total volume of 18 µL and incubated for 5 min at 70 oC.  Next, 6 µl of 5X first strand buffer, 1.5 µL 0.1M dithiothreitol (DTT), 1.5µL of dNTP mix with amino-modified nucleotides, 1µL RNAseOUT ™ (40U/µL) and 2µl of Superscript™ III reverse transcriptase (400U/µL) were incubated for 2 h at 46oC.  The aRNA template then removed by hydrolysis with 1N NaOH at 70oC for 10 min and neutralized with 0.3 N acetic acid.
The cDNA was purified using Qiagen PCR purification columns (Qiagen,Germany), according to the manufacturer’s instructions. Sample cDNAs were labelled with Cy5 (CyDye Post-labeling reactive Dye Pack Amersham Biosciences #RPN 5661) on the column for 1 hr in the dark. Samples were washed with PE buffer, eluted with 80µl of H2O.  This eluate is mixed with 400µl of PB buffer.

extract_protocol:
Total RNA was extracted from  20-30mg of muscle. Briefly, samples were homogenized in 1 ml of Trizol reagent (Invitrogen Life Technologies, Australia), and incubated at room temperature for 5 min. After addition of chloroform (200 µl), samples were incubated for 3 min at room temperature, centrifuged for 15 min (12 000 g, 4C) and the aqueous phase, containing the RNA, was precipitated with an equal volume of 100% ethanol. Total RNA was further purified through a Qiagen RNeasy Micro-column (Qiagen, Germany) according to manufacturer’s protocol. RNA was resuspended in 10µL RNase-free water.
Samples were amplified using the MessageAmp™ aRNA Kit (Ambion; Austin, Texas, USA) according to the manufactures instructions.  Briefly, 0.5µg of total RNA was reverse transcribed to form first strand of cDNA, followed immediately by the formation of the second strand of cDNA, which is then purified.  A 12 h in vitro transcription reaction was used to synthesize amplified RNA (aRNA), which was then purified and resuspended in 100µL of RNAse free water. aRNA was then ethanol precipitated by storing overnight at -20C in two volumes of 100% ethanol and 0.1 volume of 3M sodium acetate. aRNA was subsequently centrifuged at 12 000 g for 40 min at 4C, the pellet washed twice with 70% ethanol, then the aRNA resuspended in RNAse-free water to a final concentration of ~5mg/ml.

tag: Biopsy of vastus lateralis of a rested healthy control, with dietary control. No formal exercise training (<2h/wk)

source_name: Univeral human RNA

label_protocol:
Universal RNA was prepared for labelling using the Superscript™ III indirect labelling system (Invitrogen Life Technologies, Australia) where the aRNA was mixed with 1µl spike RNA, 2µl anchored oligo (dT)20 primer (2.5mg/ml) in a total volume of 18 µL and incubated for 5 min at 70 oC.  Next, 6 µl of 5X first strand buffer, 1.5 µL 0.1M dithiothreitol (DTT), 1.5µL of dNTP mix with amino-modified nucleotides, 1µL RNAseOUT ™ (40U/µL) and 2µl of Superscript™ III reverse transcriptase (400U/µL) were incubated for 2 h at 46oC.  The aRNA template then removed by hydrolysis with 1N NaOH at 70oC for 10 min and neutralized with 0.3 N acetic acid.
The cDNA was purified using Qiagen PCR purification columns (Qiagen,Germany), according to the manufacturer’s instructions. Sample cDNAs were labelled with Cy3 (CyDye Post-labeling reactive Dye Pack Amersham Biosciences #RPN 5661) on the column for 1 hr in the dark. Samples were washed with PE buffer, eluted with 80µl of H2O.  This eluate is mixed with 400µl of PB buffer.

extract_protocol: Purchase in purified form in solution. This RNA was amplified using the MessageAmp™ aRNA Kit (Ambion; Austin, Texas, USA) according to the manufactures instructions.  Briefly, 0.5µg of total RNA was reverse transcribed to form first strand of cDNA, followed immediately by the formation of the second strand of cDNA, which is then purified.  A 12 h in vitro transcription reaction was used to synthesize amplified RNA (aRNA), which was then purified and resuspended in 100µL of RNAse free water. aRNA was then ethanol precipitated by storing overnight at -20C in two volumes of 100% ethanol and 0.1 volume of 3M sodium acetate. aRNA was subsequently centrifuged at 12 000 g for 40 min at 4C, the pellet washed twice with 70% ethanol, then the aRNA resuspended in RNAse-free water to a final concentration of ~5mg/ml.

tag: Stratagene (Lot#0240515)


title: Slide 701. Pax5 -/- (Cy5) and IL-7 (Cy3).

data_processing:
The scanned microarray images were quantified using SPOT image
analysis software (http://www.hca-vision.com). Statistical analysis of the microarray data used the Bioconductor software package limma (http://www.bioconductor.org). Expression values were print-tip loess normalized, with spot quality weights used to downweight spots with unusually small or large scanned sizes (Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-273.).


title: Slide 739. Rag1-/- (Cy5) and WT (Cy3).

tag: An established Rag-/- C57BL/6 pro-B cell line was expanded in the presence of IL-7 and the stromal cell line ST-2 for 7 days as described (Nutt et al Genes Dev 11:476-491 (1997).


title: Slide 709. IL-7 (Cy5) and WT (Cy3).


title: Control subject 10

description: No additional information required

source_name: Universal human RNA

tag: Stratagene (lot#0240515)


title: Control subject 9

description: No additional information required


title: Slide 708. WT (Cy5) and IL-7 (Cy3).


title: Control subject 7

description: No additional information required

tag: Biopsy of vastus lateralis of a rested healthy control, with dietary control. No formal exrecise training (<2h/wk)


title: Control subject 3

description: No additional information required


title: Control subject 2

description: No additional information required

tag: Biopsy of vastus lateralis of a rested healthy control, with dietary control.  No formal exercise training (<2h/wk)


title: Strength trained subject 5

description: No additional information required

source_name: Human vastus lateralis, rested, strength trained

tag: Biopy of vastus lateralis of a rested athlete, with dietary control. Chronic resistance/strength training


title: Strength trained subject 4

description: No additional information required

tag: Biopsy of vastus lateralis of a rested athlete with dietary control. Chronic resistance/strength training


title: Control subject 11

description: No additional information required

tag: Biopsy of vastus lateralis of a rested healthy control, with dietary control. No forma exercise training (<2h/wk).


title: Strength trained subject 3

description: No additional information required

tag: Biopsy of vastus lateralis of a rested athlete, with dietary control. Chronic resistance/strength training.

tag: Purchased from Stratagene (Lot#0240515)


title: L-threonine producing strain vs control strain

city: Daejeon

first: Sang Yup

last: Lee

address: Dept. of Chemical & Biomolecular Engineering, KAIST, 373-1 Guseong-dong, Yuseong-gu

country: South Korea

institute: KAIST

description: In the oligo chip, 5978 of 70 mer probes that cover the genomes of E. coli K12, O157:H7 (EDL933) and O157:H7 (Sakai) are spotted in duplicates.

hyb_protocol: Cy3 and Cy5-labelled cDNA probes were concentrated by vacuum-drying, dissolved in 20 ul of hybridization solution (30% formamide, 5X SSC, 0.1% SDS, 0.1 mg/ml salmon sperm DNA) and combined. The microarray was incubated with pre-hybridization solution at 42 C for 1 hr, washed in water for 5 min, and finally centrifuged at 650 rpm for 5 min. The combined hybridization probes were denatured by incubation at 95 C for 5 min. Hybridization was performed under a cover slip with a final volume of 20 ul inside a hybridization chamber (Genomic Tree, Daejeon, Korea). After hybridization at 42 C for 16 hr, the microarray was washed for 5 min in 2 X SSC and 0.1% SDS at 42 C, 10 min in 0.1 X SSC and 0.1 % SDS at room temperature, and 4 times for 1 min in 0.1 X SSC at room temperature. Finally, the microarray was dried by centrifugation for 5 min at 650 rpm.

scan_protocol: using GenePix 4000B microarray scanner

data_processing: The mean signal intensity values of the duplicate spots were averaged and then normalized by the global normalization method. The genes showing the p-values lower than 0.05 were considered to be significant.

organism: Escherichia coli

source_name: W3110 (lacI-deleted) strain harboring pKK223-3

label_protocol: indirect labeling method: aminoallyl-modified nucleotides were incorporated during the reverse transcription

extract_protocol: using RNeasy Mini Kit

tag: control strain

source_name: L-threonine producing strain

tag: L-threonine producing strain


title: Control subject 1

description: No additional information required

source_name: Human vastus lateralis, rested, health control

tag: Biopsy of vastus lateralis of a healthy control, with dietary control.

tag: No formal exercise training (<2h/wk)


title: Strength trained subject 7

description: No additional information required

tag: Biopsy of vastua lateralis of a rested athlete, with dietary control. Chronic resistance/strength training


title: Strength trained subject 2

description: No additional information required

tag: Purcahsed from Stratagene (Lot#0240515)


title: Endurance Trained subject 2

description: No additional information required

source_name: Vastus lateralis, rested muscle, endurance training

tag: Muscle biopsy of human vastus lateralis muscle.

tag: Rested subject with dietary control.

tag: Subject chronically endurance trained

source_name: universal human RNA

tag: Purchased from Stratagene (Lot#0240515). This RNA was amplified using the MessageAmp™ aRNA Kit (Ambion; Austin, Texas, USA) according to the manufactures instructions.  Briefly, 0.5µg of total RNA was reverse transcribed to form first strand of cDNA, followed immediately by the formation of the second strand of cDNA, which is then purified.  A 12 h in vitro transcription reaction was used to synthesize amplified RNA (aRNA), which was then purified and resuspended in 100µL of RNAse free water. aRNA was then ethanol precipitated by storing overnight at -20C in two volumes of 100% ethanol and 0.1 volume of 3M sodium acetate. aRNA was subsequently centrifuged at 12 000 g for 40 min at 4C, the pellet washed twice with 70% ethanol, then the aRNA resuspended in RNAse-free water to a final concentration of ~5mg/ml.


title: Endurance trained subject 6

description: No additional information required

source_name: Human vastus lateralis, rested, endurance trained

tag: Biopsy of human vastus lateralis in a rested athlete with dietary control

tag: Chronically endurance trained


title: Endurance trained subject 3

description: No additional information required

source_name: Univeral Human RNA

tag: Purchase from Stratagene (Lot#0240515)


title: Endurance trained subject 5

description: No additional information required

tag: Biopsy of human vastus lateralis in a rested athlete with dietary control. Chronically endurance trained subject


title: Strength trained subject 1

description: No additional information required

tag: Biopsy of vastus lateralis of a rested athlete with dietary control. Chronic resistance/strength training


title: Endurance trained subject 9

description: No additional information required

tag: Biopsy of vastus lateralis of a rested athlete with dietary control. Chronically endurance trained.


title: Endurance trained subject 8

description: No additional information required

tag: Biopsy of human vastus lateralis of a rested athlete with dietary control. Chronically endurance trained subject

source_name: Univerals human RNA

tag: Purchased from Stratagene (Lot#0240515)


title: T00302445_4BNK_1

status: Public on Oct 23 2007

city: Heidelberg

first: Bibhuti

middle: Bhusan

last: Mishra

state: Heidelberg

department: Cell Biology and Biophysics

country: Germany

institute: EMBL-Heidelberg

description: SC-514 treated ,M.sm infected 4hr PI

hyb_protocol: CodeLink Expression assay protocol

scan_protocol: CodeLink Expression assay protocol

data_processing: CodeLink EXP v4.0 (http://www4.gelifesciences.com/aptrix/upp01077.nsf/Content/codelink_soft)

source_name: J774 macrophage

label_protocol: CodeLink Expression assay protocol

growth_protocol: J774 macropahges were seeded onto 24 well culture plates at 70% confluence and the following day  were infected with bacteria in the presence and absence of NFkB inhibitor.10micrograms/ml of genetamycin were added to culture medium after 1hr bacterial infection to kill the extracellular bacteria.Uninfected cells were treated the same wayeg.changing medium,adding antibiotic etc.

extract_protocol: Total RNA was isolated from J774 macrophage monolayers using Rneasy mini kit (Invitrogen).

treatment_protocol: J774 macropahge monolayers were pre-treated with NFkB inhibitor SC-514 for 1 hour and then were infected with M.smegmatis.Total RNA were isolated at 1hr and 4 hr post infection from cells treated and without NFkB inhibitor.Uninfected and untreated macrophage monolayers were treated the same way as the infected/treated samples without bacteria.

tag: SC-514 treated ,M.sm infected 4hr PI


title: T00302446_4BNK_2

description: SC-514 treated ,M.sm infected 4hr PI


title: T00302444_BNK_2

description: SC-514 treated ,M.sm infected 1hr PI

tag: SC-514 treated ,M.sm infected 1hr PI


title: Subpopulation array data, Veening et al.

city: Groningen

first: Jan-Willem

last: Veening

address: Nijenborgh 7

country: Netherlands

institute: University of Groningen

description:
See Lulko et al, 2007. (Lulko AT, Buist G, Kok J, Kuipers OP (2007) Transcriptome analysis of
temporal regulation of carbon metabolism by CcpA in Bacillus subtilis reveals
additional target genes. J Mol Microbiol Biotechnol, 12, 82-95.)

data_processing: Two biological replicates were performed and the DNA-microarray slides contained two probes of each ORF. Thus, maximally 4 datapoints for each gene were obtained. It should be noted that due to the timely centrifugation treatment, RNA quality isolated from the recovered cells was compromised, indicating that the obtained microarray data will not completely reflect the true mRNA state of both subpopulations. Also, only a relatively small amount of signal (transcripts) could be detected for the endospore containing fraction. Because of this, standard microarray data analyses could not effectively be used on these datasets. Therefore, we undertook the following approach: raw data (as submitted here) was subjected to MicroPrep analyses (van Hijum et al., 2003, MicroPreP: a cDNA microarray data pre-processing framework. Appl Bioinformatics, 2, 241-244.) (without a Lowess normalization) and genes with a coefficient of variance lower than 60% were taken into account for further analyses. These microprep data and data used for subsequent FIVA analyses (Blom et al 2007) are included in the supplemental excel file.

organism: Bacillus subtilis

source_name: Endospore fraction

growth_protocol: The strain (strain iyfp-abrB-icfp-IIA-amyE; Veening et al., 2004) was grown at 37C and continuously shaken at 245 rpm in sporulation medium. Sporulation medium was prepared as described before (Schaeffer et al., 1965) and contained dehydrated nutrient broth (0.8%), NaOH (0.5 mM), MgSO4 (1 mM), KCl (1 g/l), Ca(NO3)2 (1 mM), MnCl2 (0.01 mM) and FeSO4 (0.001 mM). Cells were harvested after 2 h into stationary growth. To separate endospore containing cells from vegetative cells, the sporulating B. subtilis culture was subjected to Ultravist gradient centrifugation (for details see Veening et al, submitted). After centrifugation, a pellet (mainly containing endospore formers) and a broad toplayer (predominantly containing vegetative cells) were clearly visible. The vegetative cells were removed from the top layer and endospore containing cells were extracted from the pellet. Total RNA was extracted from both fractions and used in subsequent DNA-microarray experiments.

tag: RNA was isolated from endospore containing cells which were separated from non-spore forming cells using buoyant density gradient centrifugation within an isogenic culture.

source_name: Vegetative cell fraction

growth_protocol: See Channel 1.

tag: RNA was isolated from vegetative cells which were separated from endospore forming cells using buoyant density gradient centrifugation within an isogenic culture.


title: Endurance trained subject 7

description: No additional information required

tag: Biopsy of human vastus lateralis in rested athlete with dietary control. Chronically endurance trained


title: T00301436_B3_4

description: Infected with M.sm 4hr post infection(PI)


title: T00302443_BNK_1

description: SC-514 treated ,M.sm infected 1hr PI


title: T00301437_B4_4

tag: Infected with M.sm 4hr post infection(PI)


title: T00280814_C1

description: uninfected/untreated control

tag: uninfected/untreated control


title: T00280820_B3_1

description: Infected with M.sm 1hr post infection(PI)


title: striatum_wildtype_5S

status: Public on Oct 22 2007

city: Bethesda

first: Alexandre

last: Kuhn

state: MD

address: 35 Convent Dr

department: NIA

institute: NIH

description: Striatal sample from a 12-month-old wild-type mouse.

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis Technical Manual)

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: Striatum (brain)

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers’ protocols

tag: Strain

value: C57BL/6; Gender:female; Age:12 months; Tissue:striatum (brain); Mouse model:wild-type


title: T00280812_B2_1

tag: Infected with M.sm 1hr post infection(PI)


title: T00280808_B1_1


title: T00280807_C3

description: uninfected/untreated control


title: striatum_wildtype_4S


title: striatum_Hdh4Q80_9S

description: Striatal sample from a 12-month-old Hdh4/Q80 mouse.

value: C57BL/6; Gender:female; Age:12 months; Tissue:striatum (brain); Mouse model:Hdh4/Q80 transgenic mice (Shelbourne et al, Hum Mol Genet 8:763-774,1999)


title: striatum_Hdh4Q80_7S


title: T00280810_B1_4


title: striatum_Hdh4Q80_8S


title: T00280806_C2

description: uninfected/untreated control


title: Rs293 Triadimefon 100uM

status: Public on Oct 21 2007

city: Research Triangle Park

first: David

last: Dix

state: NC

address: 109 TW Alexander Drive

department: ORD/NCCT

institute: US EPA

hyb_protocol: cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20).  GeneChips were hybridized at 45ºC for 16 h.  After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.

scan_protocol: Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.

data_processing: To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500.  Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA.  For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics.  Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate and an absolute difference of |1.2| or greater.  Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.

organism: Rattus norvegicus

source_name: primary hepatocytes

label_protocol: Five micrograms or purified total RNA from each sample per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).  Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer.  Biotinylated RNA (labeled cRNA) served as the microarray target.  cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.

extract_protocol: Total RNA was extracted from primary hepatocytes using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays.  For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE).  RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA).  Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays.  RNA was stored at -80ºC until labeling for microarray hybridization.

treatment_protocol: in vitro exposure, 72 hour exposure via medium


title: Rs256 Triadimefon 100uM


title: Rs256 Triadimefon 30uM


title: striatum_wildtype_6S


title: Rs304 Triadimefon 100uM


title: Rs304 Triadimefon 10uM


title: Rs256 Propiconazole 100uM


title: Rs293 Triadimefon 30uM


title: Rs256 Triadimefon 10uM


title: Rs293 Propiconazole 100uM


title: Rs304 Triadimefon 30uM


title: sDf128_sDp3

city: Vancouver

first: Martin

middle: Richard

last: Jones

state: BC

address: Room 419 NCE Building 2125 East Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

description: 3 test samples from sDp3 balanced strains individually hybridized to reference DNA (N2 Bristol)

scan_protocol: The scanner used was an Axon Scanner (Model # 4000B) .  see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Segmentation analysis based on the DNACopy package  Segmentation GFF file  Genome annotation GFF file

organism: Caenorhabditis elegans

source_name: whole animal, mixed stage

label_protocol: Cy3 and Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. Mutant DNA samples were labelled with Cy3 and the wild type DNA sample (VC196) was labelled with Cy5. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.

growth_protocol: Nematodes were grown at 200C on 150mm NGM agar plates seeded with Escherichia coli strain OP50.

extract_protocol: Animals were harvested and treated with a standard protienase K digestion. Samples were extracted using a standard phenol/chloroform protocol, treated with RNAse A for 1 hour and subjected to a second round of phenol/chloroform extraction. DNA was resuspended in water and quantified.

value: BC0049 N2 Bristol


title: Rs293 Triadimefon 10uM


title: Rs293 Propiconazole 30uM


title: Rs304 Propiconazole 30uM


title: Rs256 Propiconazole 30uM


title: sDf127_sDp3

hyb_protocol: see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.


title: Rs256 Propiconazole 10uM


title: Rs304 Propiconazole 100uM


title: sDf121_sDp3


title: Rs304 Propiconazole 10uM


title: Rs293 PCN 30uM


title: Rs293 PB  200uM


title: Rs256 PB 200uM


title: Rs304 PB 200uM


title: Rs293 Propiconazole 10uM


title: Rs293 Myclobutanil 100uM


title: Rs256 Myclobutanil 100uM


title: Rs304 PCN 30uM


title: Rs293 Myclobutanil 30uM


title: Rs304 Myclobutanil 30uM


title: ALL-SIL

status: Public on Oct 20 2007

city: Houston

first: Wei

last: Li

state: TX

address: one baylor plaza, MS BCM305

institute: Baylor College of Medicine

hyb_protocol: Standard Affymetrix Protocol, as described in GeneChip Whole Transcript Sense Target Labeling Assay Manual, Version 4 (available at http://www.affymetrix.com/support/technical/product_updates/wt_1_1_assay.affx)

data_processing: RMA

extract_protocol: Trizol and RNeasy

tag: T-ALL cell line, karotype


title: KOPTK1

scan_protocol: Standard Affymetrix Protocol, as described in GeneChip Whole Transcript Sense Target Labeling Assay Manual, Version 4 (available at http://www.affymetrix.com/support/technical/product_updates/wt_1_1_assay.affx)

source_name: Not available at atcc.org, dsmz.de or cellbank.nibio.go.jp/cellbank_e.html.  For reference see Ohnishi H et al (1995) Blood 86, 1269-1275

tag: T-ALL cell line, karyotype


title: Endothelial Replicate 1

city: sendai-city

first: Taisuke

last: Baba

state: Miyagi

address: seiryo-machi 4-1

institute: Tohoku Univ. IDAC

description: Biological replicate 1 of 2.

hyb_protocol: Hybridization were carried out on UltraGAPS coated slides in accordance with the manufacturers manual (Corning, NY)

scan_protocol: The image was captured in a GenePix 4000B (Axon Instruments, Inc. CA) The quantification of gene expression arrays was performed by Array Vision software (Imaging Research Inc., Ontario, Canada).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: Total RNA from irradiated mouse(endothelial:alpha-particle) with Cyanine-5 (red).

label_protocol: Poly-A RNA was separated using dT(25)-coupled magnetic beads (Dynal Biotech, Oslo, Norway).  Complementary DNA (cDNA) probes were generated starting with 1 ƒÊg of polyA RNA using a CyScribe First-Strand cDNA Labelling kit (Amersham Biosciences Corp., Piscataway, NJ).  cDNA from irradiated mice was labeled with Cy5.

extract_protocol: TriZol procedure

tag: Age

value: 6 weeks

tag: Tissue

value: liver

tag: Sex

source_name: Total RNA from pooled non-irradiated mice with Cyanine-3 (green).

label_protocol: Poly-A RNA was separated using dT(25)-coupled magnetic beads (Dynal Biotech, Oslo, Norway).  Complementary DNA (cDNA) probes were generated starting with 1 ƒÊg of polyA RNA using a CyScribe First-Strand cDNA Labelling kit (Amersham Biosciences Corp., Piscataway, NJ).  cDNA from non-irradiated mice was labeled with Cy3.

value: 6 weels


title: Rs304 Myclobutanil 10uM


title: Kupffer Replicate 1

description: Biological replicate 1 of 2.

source_name: Total RNA from irradiated mouse(Kupffer:alpha-particle) with Cyanine-5 (red).

value: Male


title: Rs256 Myclobutanil 30uM


title: Rs293 DMSO 0.001


title: Rs304 Myclobutanil 100uM


title: Endothelial Replicate 2

description: Biological replicate 2 of 2.


title: Rs293 Myclobutanil 10uM


title: LOUCY

label_protocol: Standard Affymetrix Protocol, as described in GeneChip Whole Transcript Sense Target Labeling Assay Manual, Version 4 (available at http://www.affymetrix.com/support/technical/product_updates/wt_1_1_assay.affx)

tag: T-ALL cell line, rare TCRgamma/delta+ T-cell line, karyotype


title: DU528

source_name: Not available at atcc.org, dsmz.de or cellbank.nibio.go.jp/cellbank_e.html.  Line developed by Kurtzberg J et al (1985) J Exp Med 162, 1561-1578

tag: T-ALL cell line, carries t(1;14)(p32;q11) leading to SCL-TCRD fusion gene, karyotype


title: Rs256 Myclobutanil 10uM


title: Rs304 DMSO 0.001


title: neutron exposured Replicate 1

description: Biological replicate 1 of 2.

source_name: Total RNA from irradiated mouse(neutron) with Cyanine-5 (red).


title: PM1_ethanol_rep3

city: Livermore

first: Anu

last: Chakicherla

state: CA

address: 7000 East Avenue, Mail Stop: L-446

institute: Lawrence Livermore National Lab

description: CHIP_ID: 20419, 21171

hyb_protocol: NimbleGen Systems, Inc. Hybriwheel technology was used to perform array hybridization. Briefly, arrays were pre-hybridized at 45°C in 50 mM MES (4-Morpholineethanesulfonic acid) buffer with 500 mM NaCl, 10 mM EDTA, and 0.005% Tween-20. Herring sperm DNA was added at 0.1 mg/ml to prevent non-specific binding.  After 15 min of pre-hybridization, 4 mg of labeled cDNA in hybridization buffer was added to arrays followed by incubation for 16-20 hr at 45°C.  Free probe was removed by conducting several wash steps, progressing from less to more stringent conditions. Bound probe was detected with Cy3-labeled streptavidin with signal amplification achieved by adding biotinylated anti-streptavidin goat antibody.

scan_protocol: The arrays were analyzed using an Axon GenePix 4000B Scanner (Molecular Devices Corp., Sunnyvale, CA).  ImageJ software was used to rotate images and double their size without interpolation. Features were extracted using GenePix 3.0 software, using a fixed feature size. The log-transformed signal (base 2) was used as the input data for analysis.

data_processing: Data analysis was performed using the R statistical package and tools available from the Bioconductor project. Data was quantile-normalized, and background corrected and summarized using the Robust Multi-array Average (RMA) method.  A linear model was fitted for each gene to estimate log-ratios between multiple target RNA samples simultaneously using the LIMMA package.  The standard errors of the estimated log-fold changes were moderated using empirical Bayes methods implemented in the LIMMA package, generating a moderated t-statistic.  P-values were obtained from this moderated t-statistic, after adjusting for multiple hypothesis testing using Benjamini and Hochberg’s method to control the false discovery rate.  We defined significant up- or downregulation as expression fold change ³2 and p-value <0.05 (actual p-values for this group were <0.01).

organism: Methylibium petroleiphilum PM1

source_name: PM1 cells grown on ethanol, aerobically

label_protocol: cDNA production and labeling were performed by NimbleGen Systems, Inc (Madison, WI).  After thawing RNA samples on ice, 10 µg total RNA was used to perform cDNA synthesis with random hexamers and SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). RNase A and H were then used to digest the RNA.  The resulting single-stranded cDNA was purified by phenol extraction and precipitated after adding 10 mg glycogen (as carrier), 0.1 volume of ammonium acetate and 2.5 volumes of 100% ethanol. The resulting pellet was dried and suspended in 30 µL water and the cDNA yield was measured by UV/visible spectrophotometry at 260 nm.  The cDNA was partially digested with DNAse I (0.2 U) at 37°C for approx. 13 min, generating 50- to 200-base fragments as observed with a Bioanalyzer (Agilent).  The fragmented cDNA was end-labeled with Biotin-N6-ddATP and terminal deoxynucleotidyl transferase (51 U) during incubation for 2 hr at 37°C.  The labeled product was concentrated to 20 µL final volume using a Microcon YM-10 10,000 MWCO filter device (Millipore, Billerica, MA) and stored at -20 °C before hybridization.

growth_protocol: Aerobic growth conditions, room temperature

extract_protocol: Aliquots of 30 mL liquid cultures were treated with RNAprotect to stabilize RNA (QIAGEN, Valencia, CA, USA) in a ratio 1 part culture to 1.6 parts reagent as outlined by the manufacturer.  RNA was subsequently extracted from the cells using a GENTRA Purescript RNA isolation kit (Gentra Systems, MN, USA) according to the manufacturer’s protocol. A DNase treatment step was included after RNA extraction in which DNase I (Roche Inc., Basel, Switzerland) was added to tubes (3 U/10 µg RNA), incubated for 30 min at 37°C, and followed by enzyme inactivation at 95°C for 5 min. RNA extracts were purified with an RNeasy Mini Kit and RNase-free DNase (QIAGEN) according to the manufacturer’s protocols.  RNA was finally eluted with 50 ml RNase-free water and stored at -80°C until cDNA synthesis. Aliquots were analyzed with a Bioanalyzer (Agilent, Santa Clara, CA), which indicated minimal degradation and concentrations ranging from 409 to 620 µg/ml, and A260/A280 ratios ranging from 1.8 to 2.1.

treatment_protocol: Treated with RNAprotect prior to harvesting cells

tag: Strain PM1


title: neutron exposured Replicate 2

description: Biological replicate 2 of 2.


title: Kupffer Replicate 2

description: Biological replicate 2 of 2.


title: PM1_MTBE_rep1

description: CHIP_ID: 20377

source_name: PM1 cells grown on MTBE, aerobically


title: PM1_MTBE_rep2

description: CHIP_ID: 20381


title: Rs256 DMSO 0.001


title: PM1_ethanol_rep2

description: CHIP_ID: 20393, 20404


title: MOLT16


title: DND41

tag: T-ALL cell line, p53 mutation, karyotype


title: PM1_MTBE_rep3

description: CHIP_ID: 20382


title: MOLT4

value: flat-moded hypertetraploid karyotype - 89-99<4n>XXYY, +4, +7, +8, +20, +20, del(6)(q16)x2, der(7)t(7;7)(p15;q11)x2 - closely related to MOLT-3. p53 mutation


title: MOLT13


title: JURKAT

value: flat-moded hypotetraploid, 8%polyploidy; 87(78-91)<4n>XX, -Y,-Y,-5,-16,-17,-22,add(2)(p21)/del(2)(p23)X2;sideline with additional der(5)t(5;10)(q11;p15),del(9)(p11)


title: SUPT11


title: SUPT13

source_name: Not available at atcc.org, dsmz.de or cellbank.nibio.go.jp/cellbank_e.html.  Line developed by Smith SD et al (1989) Blood 73, 2182-2187.

tag: T-ALL cell line, t(11;19)(q24;p13) MLL-ENL fusion gene?, karyotype


title: PM1_ethanol_rep1

description: CHIP_ID: 20392, 20397


title: RPMI8402


title: SUPT7

tag: T-ALL cell line, t(7;19)(q34;p13) LYL1-TCRB translocation, karyotype


title: CEM

tag: T-ALL cell line, submicroscopic del(q)(p32) leading to SIL-SCL fusion gene, karyotype


title: PF382

value: near-diploid, 9% near tetraploid, 15% polyploidy; 45/46(43-47),2n>X/XX,-10,+14; sideline with +add(?15)(p11), add(1)(p32)


title: BE13


title: TALL1

tag: T-ALL cell line, NRAS and p53 mutations, karyotype


title: 0401_CCRT_D9_R(N)_G(45-8)

city: TauYau

first: Yun-Shien

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: a) Normalization strategy total array b) Normalization algorithm Lowess (local weighted regression),

hyb_protocol: Hybridization Protocol Hybridization buffer: Supply by Genisphere 3DNA kits. Slide blocking: 3x SSC, 0.1% SDS, 0.1 mg/mL BSA. Prehybridization for 30 min at 50°C. wash procedure: 1x 10 min with 2x SSC, 0.2% SDS at 60oC; 1x 10 min with 2x SSC, at room temperature; 1x 10 min with 0.2x SSC at room temperature; spin-dried at 250 x g for 3 min. quantity of labeled target used 2 μg of total RNA (Genisphere 3DNA-Random Primer) first step: overnight (16 h), 25 μl, at 60 °C; second step: 2 h, 25 μl, at 60 °C. the hybridization instruments 10-slide hybridization chamber (Genetix)

scan_protocol: Axon GenePix4000A

data_processing: GenePix Pro 4.1 software (Axon Instrument, Inc.) Expected spot diameter: 140 Micrometer. PixelSize = 10

source_name: common reference (Normal)

label_protocol: Protocol Genisphere 3DNA-Random Primer Submicro Expression Array Detection Kit (category # W300130/W300140);

extract_protocol: Extract Protocol Total RNA was extracted from 2.5 ml of whole blood using the Paxgene Blood RNA System (PreAnalytiX, Hombrechtikon, CH) according to the manufacturer’s instruction. The quality and quantity of RNA was analyzed with Bioanalyzer 2100 (Agilent, Palo Alto, CA)

tag: Blood samples from 11 women with benign gynecological diseases at out-patient clinic served as normal control individuals. Pooled RNA from these samples was used as a common reference for microarray analyses.

source_name: Patient 45_8

tag: Patient 45 one month after the treatment.


title: breast tumor part_IC_rep1_2455

city: Taipei

first: Hsin-Chieh

last: Yao

address: 1,  Rd. Roosevelt,  Sec. 4

department: CHE

institute: National Taiwan University

description: Same tissue as sample 2067 but hybridized with Buffer1

scan_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0 with Agilent scanner and Feature Extraction 6.0.

data_processing: Agilent Two-Color Microarray-Based Gene Expression Analysis, version 4.0

source_name: Intraductal Carcinoma (IC)

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit, protocol version 2.0

growth_protocol: The fresh samples used for this study were immediately frozen by liquid nitrogen without any additional growth procedure applied before RNA extraction.

extract_protocol: Trizol reagent combined with Rneasy mini kit

treatment_protocol: The surgical removed tumors and non-tumor part of breast specimens were excised, collected and snap-frozen in liquid nitrogen immediately  before RNA extraction.

tag: gender

value: female

tag: tissue

value: primary tumor

source_name: Stratagene's human common reference RNA

tag: reference

value: Stratagene's human common reference RNA


title: breast tumor part_ILC_rep1_2433

description: Same tissue as sample 2045 but hybridized with Buffer1

hyb_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0

source_name: Infiltrating Lobular Carcinoma (ILC)


title: 0413_WHS_D9_R(N)_G(48_2)

source_name: Patient 48_2

tag: Patient 48 one week after the first course of chemotherapy and initiation of radiotherapy


title: 0518_CCRT_D9_R(51-1)_G(N)

description:
a) Normalization strategy
total array
b) Normalization algorithm
Lowess (local weighted regression),

hyb_protocol: Hybridization buffer: Supply by Genisphere 3DNA kits. Slide blocking: 3x SSC, 0.1% SDS, 0.1 mg/mL BSA. Prehybridization for 30 min at 50°C. wash procedure:     1x 10 min with 2x SSC, 0.2% SDS at 60oC;     1x 10 min with 2x SSC, at room temperature;     1x 10 min with 0.2x SSC at room temperature;     spin-dried at 250 x g for 3 min. quantity of labeled target used     2 µg of total RNA (Genisphere 3DNA-Random Primer) first step: overnight (16 h), 25 µl, at 60 °C;               second step: 2 h, 25 µl, at 60 °C. the hybridization instruments 10-slide hybridization chamber (Genetix)

data_processing:
GenePix Pro 4.1 software (Axon Instrument, Inc.)
Expected spot diameter: 140 Micrometer.
PixelSize = 10

source_name: Patient 51_1

label_protocol: Genisphere 3DNA-Random Primer Submicro Expression Array Detection Kit  (category # W300130/W300140);

extract_protocol: Total RNA was extracted from 2.5 ml of whole blood using the Paxgene Blood RNA System (PreAnalytiX, Hombrechtikon, CH) according to the manufacturer’s instruction. The quality and quantity of RNA was analyzed with Bioanalyzer 2100 (Agilent, Palo Alto, CA)

tag: Patient 51 before CCRT treatment


title: 0401_CCRT_D9_R(47-1)_G(N)

source_name: Patient 47_1

tag: Patient 47 before CCRT treatment


title: 0401_CCRT_D9_R(N)_G(47-1)


title: breast tumor part_IDC_rep1_2447

description: Same tissue as sample 2059 but hybridized with Buffer1

source_name: Infiltrating Ductal Carcinoma (IDC)


title: 0401_CCRT_D9_R(45-8)_G(N)

tag: Patient 45 one month after the treatment


title: 0623_CCRT_D9_R(38-4)_G(N)

source_name: Patient 38_4

tag: Patient 38 one month after the treatment


title: 0518_CCRT_D9_R(N)_G(51-1)


title: 0518_CCRT_D9_R(49-1)_G(N)

source_name: Patient 49_1

tag: Patient 49 before CCRT treatment


title: 0413_WHS_D9_R(48_2)_G(N)


title: 0623_CCRT_D9_R(37-1)_G(N)

source_name: Patient 37_1

tag: Patient 37 before CCRT treatment


title: 0401_CCRT_D9_R(N)_G(44-2)

source_name: Patient 44_2

tag: Patient 44 one week after the first course of chemotherapy and initiation of radiotherapy


title: 0401_CCRT_D9_R(45-2)_G(N)

source_name: Patient 45_2

tag: Patient 45 one week after the first course of chemotherapy and initiation of radiotherapy


title: breast nontumor part_N_rep1_2441

description: Same tissue as sample 2053 but hybridized with Buffer1

source_name: Nontumor part (also called normal(N))

value: non-tumor part of breast


title: 0518_CCRT_D9_R(N)_G(49-1)


title: 0401_CCRT_D9_R(N)_G(45-1)

source_name: Patient 45_1

tag: Patient 45 before CCRT treatment


title: 0325_CCRT_D9_R(N)_G(16-2)

source_name: Patient 16_2

tag: Patient 16 one week after the first course of chemotherapy and initiation of radiotherapy


title: 0401_CCRT_D9_R(N)_G(45-2)

source_name: common reference (Normal)


title: breast tumor part_IDC_rep1_2411

description: Same tissue as sample 2023 but hybridized with Buffer1


title: 0401_CCRT_D9_R(45-1)_G(N)


title: breast tumor part_AMC_rep1_2403

description: Same tissue as sample 2015 but hybridized with Buffer1

source_name: Atypical Medullary Carcinoma (AMC)


title: breast tumor part_IDC_rep1_2085

description: Hybridized with Buffer2


title: 0401_CCRT_D9_R(43-1)_G(N)

source_name: Patient 43_1

tag: Patient 43 before CCRT treatment


title: 0401_CCRT_D9_R(N)_G(43-1)

tag: Blood samples from 11 women with benign gynecological diseases at out-patient clinic served as normal control individuals. Pooled RNA from these samples was used as a common reference for microarray analyses.


title: 0401_CCRT_D9_R(44-2)_G(N)


title: breast tumor part_IDC_rep1_2079

description: Hybridized with Buffer2

source_name: Stratagene's human common reference RNA


title: breast tumor part_IDC_rep1_2083

description: Hybridized with Buffer2


title: breast tumor part_IDC_rep1_2081

description: Hybridized with Buffer2


title: 0325_CCRT_D9_R(16-2)_G(N)


title: breast tumor part_IDC_rep1_2077

description: Hybridized with Buffer2


title: 0623_CCRT_D9_R(N)_G(37-1)


title: breast tumor part_IDC_rep1_2065

description: Hybridized with Buffer2


title: breast tumor part_IC_rep1_2067

description: Hybridized with Buffer2

source_name: Intraductal Carcinoma (IC)


title: breast tumor part_IDC_rep1_2063

description: Hybridized with Buffer2


title: 0325_CCRT_D9_R(15-1)_G(N)

source_name: Patient 15_1

tag: Patient 15 before CCRT treatment


title: 0323_CCRT_D9_R(N)_G(26-2)

source_name: Patient 26_2

tag: Patient 26 one week after the first course of chemotherapy and initiation of radiotherapy


title: breast tumor part_IDC_rep1_2073

description: Hybridized with Buffer2

tag: gender

tag: tissue


title: breast tumor part_IDC_rep1_2061

description: Hybridized with Buffer2

tag: reference


title: 0323_CCRT_D9_R(26-2)_G(N)


title: breast tumor part_IDC_rep1_2071

description: Hybridized with Buffer2


title: 0325_CCRT_D9_R(N)_G(15-1)


title: breast tumor part_IDC_rep1_2059

description: Hybridized with Buffer2


title: 0623_CCRT_D9_R(N)_G(38-4)


title: 0323_CCRT_D9_R(N)_G(25-3)

source_name: Patient 25_3

tag: Patient 25 one week after completion of CCRT


title: 0323_CCRT_D9_R(25-3)_G(N)


title: 0323_CCRT_D9_R(N)_G(31-4)

source_name: Patient 31_4

tag: Patient 31 one month after the treatment


title: 0318_CCRT_D9_R(31-4)_G(N)


title: breast tumor part_IDC_rep1_2075

description: Hybridized with Buffer2

source_name: Infiltrating Ductal Carcinoma (IDC)


title: 0722_CCRT_D9_R(56-1)_G(N)

source_name: Patient 56_1

tag: Patient 56 before CCRT treatment


title: 0624_CCRT_D9_R(N)_G(50-2)

source_name: Patient 50_2

tag: Patient 50 one week after the first course of chemotherapy and initiation of radiotherapy


title: 0624_CCRT_D9_R(50-2)_G(N)


title: breast tumor part_IDC_rep1_2069

description: Hybridized with Buffer2


title: 0318_CCRT_D9_R(N)_G(25-1)

source_name: Patient 25_1

tag: Patient 25 before CCRT treatment


title: breast tumor part_IDC_rep1_2057

description: Hybridized with Buffer2


title: 0318_CCRT_D9_R(25-1)_G(N)


title: 0722_CCRT_D9_R(N)_G(56-1)


title: breast tumor part_IDC_rep1_2041

description: Hybridized with Buffer2


title: 0727_CCRT_D9_R(N)_G(55-2)

source_name: Patient 55_2

tag: Patient 55 one week after the first course of chemotherapy and initiation of radiotherapy


title: breast tumor part_IDC_rep1_2039

description: Hybridized with Buffer2


title: breast tumor part_IDC_rep1_2051

description: Hybridized with Buffer2


title: breast tumor part_IDC_rep1_2043

description: Hybridized with Buffer2


title: breast nontumor part_N_rep1_2053

description: Hybridized with Buffer2

source_name: Nontumor part (also called normal(N))


title: breast tumor part_IDC_rep1_2047

description: Hybridized with Buffer2


title: breast tumor part_IDC_rep1_2037

description: Hybridized with Buffer2


title: breast tumor part_IDC_rep1_2031

description: Hybridized with Buffer2


title: 0727_CCRT_D9_R(50-3)_G(N)

source_name: Patient 50_3

tag: Patient 50 one week after completion of CCRT


title: breast tumor part_IDC_rep1_2049

description: Hybridized with Buffer2

value: recurrent tumor


title: 0727_CCRT_D9_R(55-2)_G(N)


title: 0317_CCRT_D9_R(32-1)_G(N)

source_name: Patient 32_1

tag: Patient 32 before CCRT treatment


title: breast tumor part_ILC_rep1_2045

description: Hybridized with Buffer2

source_name: Infiltrating Lobular Carcinoma (ILC)


title: breast tumor part_IDC_rep1_2055

description: Hybridized with Buffer2


title: breast tumor part_IDC_rep1_2035

description: Hybridized with Buffer2


title: 0727_CCRT_D9_R(N)_G(50-3)

source_name: common reference (Normal)


title: 0317_CCRT_D9_R(N)_G(32-1)


title: breast tumor part_IDC_rep1_2033

description: Hybridized with Buffer2


title: 0317_CCRT_D9_R(N)_G(32-3)

source_name: Patient 32_3

tag: Patient 32 one week after completion of CCRT


title: 0317_CCRT_D9_R(32-3)_G(N)


title: breast tumor part_IDC_rep1_2029

description: Hybridized with Buffer2

source_name: Stratagene's human common reference RNA


title: 0311_CCRT_D9_R(N)_G(8-4)

source_name: Patient 8_4

tag: Patient 8 one month after the treatment.


title: 0311_CCRT_D9_R(N)_G(7-1)

source_name: Patient 7_1

tag: Patient 7 before CCRT treatment


title: breast tumor part_IDC_rep1_2023

description: Hybridized with Buffer2


title: breast tumor part_IDC_rep1_2025

description: Hybridized with Buffer2


title: 0311_CCRT_D9_R(21-4)_G(N)

source_name: Patient 21_4

tag: Patient 21 one month after the treatment

tag: Blood samples from 11 women with benign gynecological diseases at out-patient clinic served as normal control individuals. Pooled RNA from these samples was used as a common reference for microarray analyses.


title: 0311_CCRT_D9_R(8-4)_G(N)

tag: Patient 8 one month after the treatment


title: breast tumor part_IDC_rep1_2027

description: Hybridized with Buffer2

tag: gender


title: breast tumor part_IDC_rep1_2021

description: Hybridized with Buffer2

tag: tissue


title: 0804_CCRT_D9_R(57-1)_G(N)

source_name: Patient 57_1

tag: Patient 57 before CCRT treatment


title: 0311_CCRT_D9_R(8-2)_G(N)

source_name: Patient 8_2

tag: Patient 8 one week after the first course of chemotherapy and initiation of radiotherapy


title: 0804_CCRT_D9_R(N)_G(57-1)


title: 0804_CCRT_D9_R(N)_G(58-2)

source_name: Patient 58_2

tag: Patient 58 one week after the first course of chemotherapy and initiation of radiotherapy


title: breast tumor part_MCB_rep1_1715

description: Hybridized with Buffer1

source_name: Metaplastic Carcinoma of Breast (MCB)

tag: reference


title: breast tumor part_MCB_rep1_1763

description: Hybridized with Buffer1


title: breast tumor part_MCB_rep1_1779

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_2017

description: Hybridized with Buffer2

source_name: Infiltrating Ductal Carcinoma (IDC)


title: 0826_CCRT_D9_R(49-4)_G(N)

source_name: Patient 49_4

tag: Patient 49 one month after the treatment.


title: breast tumor part_AMC_rep1_2015

description: Hybridized with Buffer2

source_name: Atypical Medullary Carcinoma (AMC)


title: 0826_CCRT_D9_R(N)_G(61-1)

source_name: Patient 61_1

tag: Patient 61 before CCRT treatment


title: breast tumor part_IDC_rep1_2019

description: Hybridized with Buffer2


title: 0804_CCRT_D9_R(58-2)_G(N)

source_name: Patient 58-2


title: 0311_CCRT_D9_R(N)_G(8-2)


title: 0826_CCRT_D9_R(61-2)_G(N).

source_name: Patient 61_2

tag: Patient 61 one week after the first course of chemotherapy and initiation of radiotherapy


title: 0831_CCRT_D9_R(17-1)_G(N)

source_name: Patient 17_1

tag: Patient 17 before CCRT treatment


title: 0826_CCRT_D9_R(N)_G(49-4)

source_name: common reference (Normal)


title: 0826_CCRT_D9_R(61-1)_G(N)


title: breast tumor part_ILC_rep1_1709

description: Hybridized with Buffer1

source_name: Infiltrating Lobular Carcinoma (ILC)


title: 0826_CCRT_D9_R(N)_G(61-2)


title: 0311_CCRT_D9_R(7-1)_G(N)


title: breast tumor part_PT_rep1_1699

description: Hybridized with Buffer1

source_name: Phyllodes Tumor(PT)

source_name: Stratagene's human common reference RNA


title: 0309_CCRT_D9_R(N)_G(21_2)

source_name: Patient 21_2

tag: Patient 21 one week after the first course of chemotherapy and initiation of radiotherapy


title: breast tumor part_MCB_rep1_1681

description: Hybridized with Buffer1


title: 0831_CCRT_D9_R(23-1)_G(N)

source_name: Patient 23-1

tag: Patient 23-1 before CCRT treatment


title: 0915_CCRT_D9_R(N)_G(57-3)

source_name: Patient 57-3

tag: Patient 57 one week after completion of CCRT


title: 0923_CCRT_D9_R(N)_G(55-3)

source_name: Patients 55_3

tag: Patients 55 one week after completion of CCRT


title: 0915_CCRT_D9_R(N)_G(40-1)

source_name: Patient 40_1

tag: Patient 40 before CCRT treatment


title: 0831_CCRT_D9_R(N)_G(17-1)

tag: Blood samples from 11 women with benign gynecological diseases at out-patient clinic served as normal control individuals. Pooled RNA from these samples was used as a common reference for microarray analyses.

tag: Patient 17_1 before CCRT treatment


title: 0915_CCRT_D9_R(57-3)_G(N)

source_name: Patient 57_3


title: 0831_CCRT_D9_R(N)_G(23-1)

tag: Patient 23_1 before CCRT treatment


title: 0909_CCRT_D9_R(40-1)_G(N)

tag: Patient 40_1 before CCRT treatment


title: 0204_WTH_D9_R(N)_G(20-3)

source_name: Patient 20_3

tag: Patient 20 one week after completion of CCRT


title: 0309_CCRT_D9_R(N)_G(21_1)

source_name: Patient 21_1

tag: Patient 21 before CCRT treatment


title: 0309_CCRT_D9_R(21_1)_G(N)


title: breast tumor part_MC_rep1_1663

description: Hybridized with Buffer1

source_name: Mucinous Carcinoma (MC)

tag: gender

tag: tissue


title: 1012_CCRT_D9_R(N)_G(57-4)

source_name: Patient 57-4

tag: Patient 57-4 one month after the treatment


title: 1021_CCRT_D9_R(N)_G(56-4)

source_name: Patient 56_4

tag: Patient 56 one month after the treatment


title: 0309_CCRT_D9_R(21_2)_G(N)


title: 0204_WTH_D9_R(N)_G(20-2)

source_name: Patient 20_2

tag: Patient 20 one week after the first course of chemotherapy and initiation of radiotherapy


title: 1104_CCRT_D9_R(N)_G(62-3)

source_name: Patient 62-3

tag: Patient 62 one week after completion of CCRT