title: Mening UNSTIM WB NP 6a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20583.gif
Infection: N
name: 20583_Infection

tag: Common Reference 2 round amplification 2 ug

source_name: Mening UNSTIM WB NP 6a

tag: Mening UNSTIM WB NP 6a


title: Mening SWB WB NP 3a

status: Public on Dec 30 2005

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20597.gif
Infection: Y
name: 20597_Infection

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

molecule: total RNA

organism: Homo sapiens

source_name: Common Reference 2 round amplification 2 ug

source_name: Mening SWB WB NP 3a

tag: Mening SWB WB NP 3a


title: Mening UNSTIM WB SW 6b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20543.gif
Infection: N
name: 20543_Infection

source_name: Mening UNSTIM WB SW 6b

tag: Mening UNSTIM WB SW 6b


title: Mening UNSTIM WB NP 0a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20585.gif
Infection: N
name: 20585_Infection

source_name: Mening UNSTIM WB NP 0a

tag: Mening UNSTIM WB NP 0a


title: Mening UNSTIM WB SW 3b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20580.gif
Infection: N
name: 20580_Infection

source_name: Mening UNSTIM WB SW 3b

tag: Mening UNSTIM WB SW 3b


title: Mening SWB WB SW 6a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20567.gif
Infection: Y
name: 20567_Infection

source_name: Mening SWB WB SW 6a

tag: Mening SWB WB SW 6a


title: Mening UNSTIM WB SW 1a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20544.gif
Infection: N
name: 20544_Infection

source_name: Mening UNSTIM WB SW 1a

tag: Mening UNSTIM WB SW 1a


title: Mening UNSTIM WB NP 3a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20596.gif
Infection: N
name: 20596_Infection

source_name: Mening UNSTIM WB NP 3a

tag: Mening UNSTIM WB NP 3a


title: Mening UNSTIM WB NP 24b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20565.gif
Infection: N
name: 20565_Infection

source_name: Mening UNSTIM WB NP 24b

tag: Mening UNSTIM WB NP 24b


title: Mening SWB WB NP 6b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20582.gif
Infection: Y
name: 20582_Infection

source_name: Mening SWB WB NP 6b

tag: Mening SWB WB NP 6b


title: Mening UNSTIM WB NP 12a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20568.gif
Infection: N
name: 20568_Infection

source_name: Mening UNSTIM WB NP 12a

tag: Mening UNSTIM WB NP 12a


title: Mening Unstim WB SW 24a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20528.gif
Infection: N
name: 20528_Infection

source_name: Mening Unstim WB SW 24a

tag: Mening Unstim WB SW 24a


title: Mening SWB WB SW 24a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20790.gif
Infection: Y
name: 20790_Infection

source_name: Mening SWB WB SW 24a

tag: Mening SWB WB SW 24a


title: Mening UNSTIM WB SW 3a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20578.gif
Infection: N
name: 20578_Infection

source_name: Mening UNSTIM WB SW 3a

tag: Mening UNSTIM WB SW 3a


title: Mening SWB WB NP 3b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20590.gif
Infection: Y
name: 20590_Infection

source_name: Mening SWB WB NP 3b

tag: Mening SWB WB NP 3b


title: Mening UNSTIM WB SW 1b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20593.gif
Infection: N
name: 20593_Infection

source_name: Mening UNSTIM WB SW 1b

tag: Mening UNSTIM WB SW 1b


title: Mening SWB WB SW 3a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20594.gif
Infection: Y
name: 20594_Infection

tag: Common Reference 2 round amplification 2 ug

source_name: Mening SWB WB SW 3a

tag: Mening SWB WB SW 3a


title: Mening UNSTIM WB SW 0b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20595.gif
Infection: N
name: 20595_Infection

source_name: Common Reference 2 round amplification 2 ug

source_name: Mening UNSTIM WB SW 0b

tag: Mening UNSTIM WB SW 0b


title: Mening SWB WB SW 1a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20592.gif
Infection: Y
name: 20592_Infection

source_name: Mening SWB WB SW 1a

tag: Mening SWB WB SW 1a


title: Mening SWB WB SW 24b2

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20539.gif
Infection: Y
name: 20539_Infection

source_name: Mening SWB WB SW 24b2

tag: Mening SWB WB SW 24b2


title: EC12n095 RpoE 60 min Time course 4

status: Public on Oct 13 2005

city: San Francisco

first: Virgil

middle: Arthur

last: Rhodius

address: Genentech Hall, 600 16th Street

department: Microbiology and Immunology

institute: UCSF

description: Wild type vs RpoE (SigmaE) 60 min after overexpression

hyb_protocol: cDNA from 16 ug total RNA, 15 ug poly(dI-dC), 3xSSC, 25 mM Hepes (pH7), 0.225% SDS. Samples hybridized on array under a lifterslip for 12 hrs at 65 degrees C

scan_protocol: Slides scanned using GenePix 4000B scanner (Axon). TIFF images analyzed using GENEPIX 3.0 software (Axon).

data_processing: Data filtered for PCR success, >3x local background and spot quality (GenePix Flag). Normalized using Lowess smoothing from MA plot

organism: Escherichia coli

source_name: Wild type control (60 min)

label_protocol: Indirect labeling method as described in Khodursky et al (2003; Methods Mol Biol 224:61-78)

growth_protocol: M9 minimal complete media, cultures grown aerobically at 30 degrees C in a gyratory water bath shaking at 240 rpm

extract_protocol: Culture samples for microarray analysis were added to ice-cold 5% water-saturated phenol in ethanol solution, centrifuged at 6,600 g and the cell pellets flash frozen in liquid N2 before storing at -80 degrees C until required. Total RNA was isolated from the stored cell pellets using the hot phenol method, and labeled Cy3 and Cy5 cDNA was prepared from 16 ug total RNA with 10 ug random hexamer (Integrated DNA Technologies, Inc., Coralville, IA, USA).

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 60 min after induction

tag: MG1655 rpoHp3::lacZ delta lacX74/ptrc99A (control vector)

source_name: RpoE induced (60 min)

tag: MG1655 rpoHp3::lacZ delta lacX74/pLC245 (vector carrying inducible Ptrc::rpoE)


title: EC12n094 RpoE 30 min Time course 4

description: Wild type vs RpoE (SigmaE) 30 min after overexpression

source_name: Wild type control (30 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 30 min after induction

source_name: RpoE induced (30 min)


title: EC8n051 RpoE 20 min Time course 3

description: Wild type vs RpoE (SigmaE) 20 min after overexpression

source_name: Wild type control (20 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 20 min after induction

source_name: RpoE induced (20 min)


title: Mening SWB WB SW 3b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20576.gif
Infection: Y
name: 20576_Infection

source_name: Mening SWB WB SW 3b

tag: Mening SWB WB SW 3b


title: EC8n050 RpoE 10min Time course 3

description: Wild type vs RpoE (SigmaE) 10 min after overexpression

source_name: Wild type control (10 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 10 min after induction

source_name: RpoE induced (10 min)


title: EC12n093 RpoE 20 min Time course 4


title: EC8n021 RpoE 2.5 min Time course 3

description: Wild type vs RpoE (SigmaE) 2.5 min after overexpression

source_name: Wild type control (2.5 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 2.5 min after induction

source_name: RpoE induced (2.5 min)


title: EC12n090 RpoE 2.5 min Time course 4


title: Mening SWB WB SW 1b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20573.gif
Infection: Y
name: 20573_Infection

source_name: Mening SWB WB SW 1b

tag: Mening SWB WB SW 1b


title: EC12n092a RpoE 10 min Time course 4


title: ENCODE ChIP-chip for BAF170 on Human Hela S3 Cells Sample 1 (unpublished)

status: Public on Nov 04 2005

type: genomic

city: Woodbridge

first: Can

last: Bruce

state: CT

address: 5 Chestnut Lane

institute: Sciomix

description:
HeLa S3 cells were grown in suspension in Joklik’s modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbecco’s PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, four 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with either 20 ug of anti-BAF170  (H-116) rabbit polyclonal antibody (Santa Cruz sc-10757) or 20 ug of normal rabbit IgG (Santa Cruz sc-2027) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.
For NimbleGen arrays, ChIP DNA prepared from 1.5 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from BAF170-immunoprecipitated cells) or Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG- immunoprecipitated cells). The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Arrays were scanned on an Axon 4000B scanner.

hyb_protocol: not provided

scan_protocol: not provided

data_processing: no processing; value = log_2( Signal for Cy5 / Signal for Cy3)

molecule: genomic DNA

source_name: BAF170 ChIP HeLa S3 Cells

label_protocol: not provided

extract_protocol: not provided

tag: HeLa S3 Cells

source_name: Input DNA, total genomic DNA from HeLa S3 Cells


title: ENCODE ChIP-chip for BAF170 on Human Hela S3 Cells Sample 3 (unpublished)


title: EC12n101 RpoE 0 min Time course 3

description: Wild type vs RpoE (SigmaE) 0 min after overexpression

source_name: Wild type control (0 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 0 min after induction

source_name: RpoE induced (0 min)


title: EC7n071 RpoE 60 min Time course 1


title: EC7n019 RpoE 15 min Time course 1

description: Wild type vs RpoE (SigmaE) 15 min after overexpression

source_name: Wild type control (15 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 15 min after induction

source_name: RpoE induced (15min)


title: EC7n066 RpoE 15 min Time course 2

source_name: RpoE induced (15 min)


title: EC7n068 RpoE 60 min Time course 2

source_name: Wild type control (60 min)

source_name: RpoE induced (60 min)


title: ENCODE ChIP-chip for BAF170 on Human Hela S3 Cells Sample 2 (unpublished)


title: Mening SWB WB NP 12b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20558.gif
Infection: Y
name: 20558_Infection

source_name: Common Reference 2 round amplification 2 ug

source_name: Mening SWB WB NP 12b

tag: Mening SWB WB NP 12b


title: ENCODE ChIP-chip for BAF170 on Human Hela S3 Cells Sample 4 (unpublished)

source_name: Normal Rabbit IgG ChIP HeLa S3 Cells


title: ENCODE ChIP-chip for BAF155 on Human Hela S3 Cells Sample 2 (unpublished)

description:
HeLa S3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbecco’s PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, four 30-second pulses) to an average of 700 bp as verified on1.5% agarose gel. Clarified lysates were agitated overnight at 4C with either 20 ug of anti-BAF155  (H-76) rabbit polyclonal antibody (Santa Cruz sc-10756) or 20 ug of normal rabbit IgG (Santa Cruz sc-2027) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.
For NimbleGen arrays, ChIP DNA prepared from 1.5 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from BAF155-immunoprecipitated cells) or Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG- immunoprecipitated cells). The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Arrays were scanned on an Axon 4000B scanner.

source_name: BAF155 ChIP HeLa S3 Cells


title: EC12n096 RpoE 0 min Time course 4


title: ENCODE ChIP-chip for BAF155 on Human Hela S3 Cells Sample 3 (unpublished)

description:
HeLa S3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbecco’s PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, four 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with either 20 ug of anti-BAF155  (H-76) rabbit polyclonal antibody (Santa Cruz sc-10756) or 20 ug of normal rabbit IgG (Santa Cruz sc-2027) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.
For NimbleGen arrays, ChIP DNA prepared from 1.5 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from BAF155-immunoprecipitated cells) or Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG- immunoprecipitated cells). The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Arrays were scanned on an Axon 4000B scanner.


title: EC8n052 RpoE 30 min Time course 3

source_name: Wild type control (30 min)

source_name: RpoE induced (30 min)


title: Mening SWB WB NP 12a

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20556.gif
Infection: Y
name: 20556_Infection

source_name: Mening SWB WB NP 12a

tag: Mening SWB WB NP 12a


title: EC12n091 RpoE 5 min Time course 4

description: Wild type vs RpoE (SigmaE) 5 min after overexpression

source_name: Wild type control (5 min)

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 5 min after induction

source_name: RpoE induced (5 min)


title: ENCODE ChIP-chip for BAF155 on Human Hela S3 Cells Sample 4 (unpublished)

source_name: Input DNA, total genomic DNA from HeLa S3 Cells


title: EC7n067 RpoE 30 min Time course 2


title: ENCODE ChIP-chip for BAF155 on Human Hela S3 Cells Sample 1 (unpublished)

description:
HeLa S3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented wit5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbecco’s PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, four 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with either 20 ug of anti-BAF155  (H-76) rabbit polyclonal antibody (Santa Cruz sc-10756) or 20 ug of normal rabbit IgG (Santa Cruz sc-2027) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.
For NimbleGen arrays, ChIP DNA prepared from 1.5 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from BAF155-immunoprecipitated cells) or Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG- immunoprecipitated cells). The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Arrays were scanned on an Axon 4000B scanner.


title: EC8n022 RpoE 5 min Time course 3


title: EC8n053 RpoE 60 min Time course 3


title: AC1500 (OD 0.6) replicate 2

status: Public on Aug 11 2005

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32840.gif

organism: Streptococcus pneumoniae

source_name: 1 ug mixed AC353

tag: 1 ug mixed AC353


title: AC1500 (OD 0.6) replicate 1

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32839.gif


title: AC1481 (OD 0.6) replicate 1

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32831.gif


title: AC1481 (OD 0.6) replicate 2

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32832.gif


title: AC1481 (OD 0.4) replicate 2

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32830.gif


title: AC1481 (OD 0.2) replicate 2

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32828.gif


title: AC1481 (OD 0.4) replicate 1

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32829.gif


title: EC7n018 RpoE 5 min Time course 1

source_name: RpoE induced (5min)


title: AC1500 (OD 0.4) replicate 1

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32837.gif


title: #13 Dll1tm1Gos pool - Wildtype pool

status: Public on Mar 01 2005

city: Munich - Neuherberg

first: Johannes

last: Beckers

state: Bavaria

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: GSF - National Research Center

description:
Mice were kept on an isogenic 129SvJ background. Embryos were obtained from timed pregnancies and dissected at E10.5.
9 dual-color DNA-chip hybridizations of cDNAs from RNA pools of wt and homozygous Dll1tm1Gos embryos respectively were made. Total RNA from pooled samples was obtained according to manufacturer’s protocols using RNeasy Mini or Midi kits (Qiagen). 20µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the labelling protocol supplied by Clontech with the Atlas Glass Mouse 1 array. Hybridisation and washing was performed as suggested by Clontech.
Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Mean intensities with subtracted background were normalised so that the median of their ratios has become 1.

organism: Mus musculus

source_name: RNA of E10.5 wildtype pool

source_name: RNA of E10.5 Dll1tm1Gos pool


title: AC1481 (OD 0.8) replicate 2

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32834.gif


title: AC1500 (OD 0.8) replicate 2

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32842.gif


title: AC1481 (OD 0.2) replicate 1

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32827.gif


title: AC1500 (OD 0.2) replicate 2

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32836.gif


title: #12 Dll1tm1Gos pool - Wildtype pool


title: AC1500 (OD 0.2) replicate 1

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32835.gif


title: AC1481 (OD 0.8) replicate 1

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32833.gif


title: 370 G1

status: Public on Mar 09 2005

city: Chicago

first: M Rosario

last: Hernandez

state: IL

address: 330 Chicago Avenue

department: Ophthalmology

institute: Northwestern University

description:
Astrocytes from optic nerve head of 56-year-old woman with glaucoma, left eye
Lot batch =

source_name: Primary optic nerve head astrocytes


title: 369 N1

description: Astrocytes from optic nerve head of 46-year-old woman, left eye

source_name: Primary Optic nerve head astrocytes


title: AC1500 (OD 0.8) replicate 1

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32841.gif


title: #9 Dll1tm1Gos pool - Wildtype pool


title: Mening UNSTIM WB NP 3b

description:
Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20591.gif
Infection: N
name: 20591_Infection

source_name: Mening UNSTIM WB NP 3b

tag: Mening UNSTIM WB NP 3b


title: AC1500 (OD 0.4) replicate 2

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32838.gif


title: #8 Dll1tm1Gos pool - Wildtype pool


title: #7 Dll1tm1Gos pool - Wildtype pool


title: #10 Dll1tm1Gos pool - Wildtype pool

description:
Mice were kept on an isogenic 129SvJ background. Embryos were obtained from timed pregnancies and dissected at E10.5.
9 dual-color DNA-chip hybridizations of cDNAs from RNA pools of wt and Dll1tm1Gos embryos respectively were made. Total RNA from pooled samples was obtained according to manufacturer’s protocols using RNeasy Mini or Midi kits (Qiagen). 20µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the labelling protocol supplied by Clontech with the Atlas Glass Mouse 1 array. Hybridisation and washing was performed as suggested by Clontech.
Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Mean intensities with subtracted background were normalised so that the median of their ratios has become 1.


title: #11 Dll1tm1Gos pool - Wildtype pool


title: #4 Dll1tm1Gos pool - Wildtype pool

description:
Mice were kept on an isogenic 129SvJ background. Embryos were obtained from timed pregnancies and dissected at E10.5.
4 dual-color DNA-chip hybridizations of cDNAs from RNA pools of wt and homozygous Dll1tm1Gos embryos respectively were made. Total RNA from pooled samples was obtained according to manufacturer’s protocols using RNeasy Mini or Midi kits (Qiagen). 20µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30µl hybridisation buffer (6xSSC, 0,5%SDS 5xDenhardt’s solution and 50% formamide) and mixed with 30µl of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre-hybridised microarray, covered with cover slip, placed into a hybridization chamber (Gene Machines) and immersed in a thermostatic bath at 42°C for 18-20 hours.
Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Mean intensities with subtracted background were normalised so that the median of their ratios has become 1.


title: #3 Dll1tm1Gos pool - Wildtype pool


title: #6 Dll1tm1Gos pool - Wildtype pool


title: #5 Dll1tm1Gos pool - Wildtype pool


title: BXD 28_M7SS02080623

status: Public on Dec 02 2004

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD28 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD28
Keywords = a cross of C57BL/6 and DBA/2 mice

source_name: hematopoietic stem cells, stem cells:Lin-Sca+kit+


title: BXD 28_M7SS02080624


title: #2 Dll1tm1Gos pool - Wildtype pool


title: 12671094|BL6 vs. FVBN liver

status: Public on Jul 28 2005

description:
Simple annotation: myc, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52372.gif

source_name: C57BL/6 mouse female genomic DNA

tag: C57BL/6 mouse female genomic DNA

source_name: FVBN mouse male liver DNA

tag: FVBN mouse male liver DNA


title: #1 Dll1tm1Gos pool - Wildtype pool


title: 12671469|BL6 vs. B1011.onoffon

description:
Simple annotation: myc, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52364.gif

source_name: C57BL/6 mouse male genomic DNA

tag: C57BL/6 mouse male genomic DNA

source_name: B1011 mouse male tumor DNA

tag: B1011 mouse male tumor DNA


title: BXD 14_M7SS02080622

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD14 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD14
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 34_M7SS02080618

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD34 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD34
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 1_M7SS02080616

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD1 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD1
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 34_M7SS02080617


title: BXD 5_M7SS02080619

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD5 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD5
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 5_M7SS02080620


title: BXD 1_M7SS02080615


title: BXD 14_M7SS02080621


title: EC7n065 RpoE 5 min Time course 2

description: Wild type vs RpoE (SigmaE) 5 min after overexpression


title: BXD 16_M7SS02080613

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD16 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD16
Keywords = a cross of C57BL/6 and DBA/2 mice


title: 12671467|BL6 vs. B101110

description:
Simple annotation: myc, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52362.gif


title: 12671468|BL6 vs. B1011P1

description:
Simple annotation: myc, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52363.gif


title: 12671470|BL6 vs. B1011P4.onoff

description:
Simple annotation: myc, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52368.gif


title: 12671471|BL6 vs. B1011P4.onoffonoff

description:
Simple annotation: myc, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52370.gif


title: BXD 16_M7SS02080614


title: BXD 39_M7SS02080609

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD39 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD39
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 2_M7SS02080612

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD2 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD2
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 39_M7SS02080610


title: BXD 2_M7SS02080611


title: BXD 9_M7SS02080608

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD9 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD9
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 9_M7SS02080607


title: BXD 19_M7SS02080605

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD19 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD19
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 18_M7SS02080602

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD18 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD18
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 21_M7SS02080603

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD21 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD21
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD32_M7SS02042219

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD32 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD32
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 19_M7SS02080606


title: BXD32_M7SS02042220


title: BXD40_M7SS02042215

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD40 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD40
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 18_M7SS02080601


title: BXD42_M7SS02042218

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD42 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD42
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD 21_M7SS02080604


title: BXD42_M7SS02042217


title: BXD40_M7SS02042216


title: BXD38_M7SS02042213

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD38 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD38
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD38_M7SS02042214


title: BXD33_M7SS02042212

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD33 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD33
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD31_M7SS02042209

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD31 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD31
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD12_M7SS02042208

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD12 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD12
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD11_M7SS02042206

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD11 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD11
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD33_M7SS02042211


title: BXD8_M7SS02042204

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD8 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD8
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD11_M7SS02042205


title: BXD12_M7SS02042207


title: BXD8_M7SS02042203


title: BXD6_M7SS02042202

description:
Bone marrow from female BXD recombinant inbred mice between 3 and 6 months of age were flushed from the femurs and tibiae of three mice and pooled, for each sample. After standard erythrocyte lysis nucleated cells were were stained with a panel of biotinylated lineage-specific antibodies (Mouse Lineage Panel, containing anti-CD3e, anti-CD45R/B220, anti-CD11b (Mac-1), anti-TER119 (Ly-76), anti-Gr-1 (Ly-6G), Pharmingen, San Diego, CA), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen).  Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells.  Cells were washed twice, and incubated for 30 minutes with streptavidin-PE (Pharmingen). After two washes cells were resuspended in PBS with 0,2% BSA, and purified using a MoFlo flowcytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PE-fluorescence intensity. Cells was immediately collected in RNA lysis buffer.
This sample is from recombinant inbred strain BXD6 ; a cross of C57BL/6 and DBA/2 mice
Keywords = This sample is from recombinant inbred strain BXD6
Keywords = a cross of C57BL/6 and DBA/2 mice


title: BXD31_M7SS02042210


title: BXD6_M7SS02042201


title: 2e liver, mouse 2 - kidney pool

status: Public on Oct 15 2004

description:
Breeding of wildtype C3HeB/FeJ mice was under specified pathogen free (spf) conditions. Left kidney and dorsal lobe of the liver were collected at the age of 105 days (+/-5 days) from male mice.
16 dual-color DNA-chip hybridizations of cDNAs from three age-matched male mice were made. For each individual mouse 6 or 4 replicate hybridizations were done. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). 20µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30µl hybridisation buffer (6xSSC, 0,5%SDS 5xDenhardt’s solution and 50% formamide) and mixed with 30µl of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre-hybridised microarray, covered with cover slip, placed into a hybridization chamber (Gene Machines) and immersed in a thermostatic bath at 42°C for 18-20 hours.
Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with subtracted background were normalised so that the median of their ratios has became 1.

Keywords = kidney
Keywords = liver
Keywords = C3HeB/FeJ

source_name: RNA of liver (mouse 2)

source_name: RNA pool of 5 mouse kidneys (K1-K5)


title: 3d liver mouse 3 - kidney pool

source_name: RNA of liver (mouse 3)


title: 3a kidney mouse 3 - liver pool

source_name: RNA of kidney (mouse 3)

source_name: RNA pool of 5 mouse livers (L1-L5)


title: 2d liver, mouse 2 - kidney pool


title: 2f liver, mouse 2 - kidney pool


title: 3c liver mouse 3 - kidney pool


title: 3b liver mouse 3 - kidney pool


title: 1b kidney, mouse 1 - liver pool

description:
Breeding of wildtype C3HeB/FeJ mice was under specified pathogen free (spf) conditions. Left kidney and dorsal lobe of the liver were collected at the age of 105 days (+/-5 days) from male mice.
16 dual-color DNA-chip hybridizations of cDNAs from three age-matched male mice were made. For each individual mouse 6 or 4 replicate hybridizations were done. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). 20µg total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30µl hybridisation buffer (6xSSC, 0,5%SDS 5xDenhardt’s solution and 50% formamide) and mixed with 30µl of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre-hybridised microarray, covered with cover slip, placed into a hybridization chamber (Gene Machines) and immersed in a thermostatic bath at 42°C for 18-20 hours.
Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with subtracted background were normalised so that the median of their ratios has became 1.
Keywords = kidney
Keywords = liver
Keywords = C3HeB/FeJ

source_name: RNA of kidney (mouse 1)


title: 1f liver, mouse 1 - kidney pool

source_name: RNA of liver (mouse 1)


title: 1e liver, mouse 1 - kidney pool


title: 1c kidney, mouse 1 - liver pool


title: 2b kidney, mouse 2 - liver pool

source_name: RNA of kidney (mouse 2)


title: 1a kidney, mouse 1 - liver pool


title: 1d liver, mouse 1 - kidney pool


title: 2a kidney, mouse 2 - liver pool


title: 2c kidney, mouse 2 - liver pool


title: A1: ERBB2-transfected versus wildtype mouse fibroblasts, preparation A, repetition 1

status: Public on Jun 04 2004

description:
The parental mouse fibroblast cell line NIH3T3 was obtained from the American tissue type culture collection (ATCC). NIH3T3 cells constitutively overexpressing the human HER-2/NEU (ERBB2) (cytomegalovirus (CMV)-HER2/NEU+) have been recently described (Herrmann et al., 2004). Both, un-transfected NIH3T3 (HER-2/NEU-) and HER-2/NEU transfected (HER-2/NEU+) cells were routinely maintained in Dulbecco’s modified Eagle’s medium (DMEM, PAN, Aidenbach, Germany) supplemented with 10 % fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 ug/ml streptomycin. Cells were cultured at 37 C in 5 % CO2 humidified air.
Approximately 2 x 10^6 cells/T25 flask were harvested and total cellular RNA from HER2/NEU- and HER2/NEU+ cells was isolated according to manufacturer’s protocols using RNeasy kits (Qiagen). 20ug total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 according the TIGR protocol. Labelled cDNA was dissolved in 30ul hybridisation buffer (6x SSC, 0,5% SDS 5 fold Denhardt’s solution and 50% formamide) and mixed with 30ul of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre-hybridised microarray, covered with cover slip, placed into a hybridisation chamber (Gene Machines) and immersed in a thermostatic bath at 42C for 18-20 hours.
Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with subtracted background were normalised so that the median of their ratios has became 1.
Keywords = Her2, Erbb2, Neu, transfected, fibroblasts

source_name: NIH3T3, Cy5

source_name: Erbb2+ fibroblasts, Cy3


title: B1: ERBB2-transfected versus wildtype mouse fibroblasts, preparation B, repetition 1


title: W4.1

status: Public on May 27 2004

description:
Mice were bred on a mixed genetic background of C57BL/6 and 129Sv. Kidneys were collected from male animals at the age of 88 (+- 2) days after birth. Mice were killed by cervical dislocation between 8am and 10am to minimise effects of the circadian rhythm on gene expression.
Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). 20ug total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30ul hybridisation buffer (6x SSC, 0,5% SDS 5 fold Denhardt’s solution and 50% formamide) and mixed with 30ul of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre-hybridised microarray, covered with cover slip, placed into a hybridisation chamber (Gene Machines) and immersed in a thermostatic bath at 42C for 18-20 hours.
Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with subtracted background were normalised so that the median of their ratios has became 1.
Keywords = kidney
Keywords = C57BL/6
Keywords = 129Sv
Keywords = WT
Keywords = wild typ
Keywords = normal variations

source_name: right kidney of WT male mouse W4

source_name: right kidney of WT male mouse W5


title: W4.2


title: W3.3

source_name: right kidney of WT male mouse W3


title: B2: ERBB2-transfected versus wildtype mouse fibroblasts, preparation B, repetition 2

source_name: Erbb2+ fibroblasts, Cy5

source_name: NIH3T3, Cy3


title: A2: ERBB2-transfected versus wildtype mouse fibroblasts, preparation A, repetition 2


title: A3: ERBB2-transfected versus wildtype mouse fibroblasts, preparation A, repetition 3


title: W3.4


title: W4.4


title: W3.1


title: W3.2


title: W1.4

description:
Mice were bred on a mixed genetic background of C57BL/6 and 129Sv. Kidneys were collected from male animals at the age of 88 (+- 2) days after birth. Mice were killed by cervical dislocation between 8am and 10am to minimise effects of the circadian rhythm on gene expression.
Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). 20ug total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30ul hybridisation buffer (6x SSC, 0,5% SDS 5 fold Denhardt’s solution and 50% formamide) and mixed with 30ul of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre-hybridised microarray, covered with cover slip, placed into a hybridisation chamber (Gene Machines) and immersed in a thermostatic bath at 42C for 18-20 hours.
Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with subtracted background were normalised so that the median of their ratios has became 1.
Keywords = kidney, C57BL/6, 129Sv, WT, wild typ, normal variations

source_name: right kidney of WT male mouse W1


title: W2.1

source_name: right kidney of WT male mouse W2


title: W2.3


title: W4.3


title: W2.2


title: W2.4


title: W1.2


title: Pept2 KO - K4.3

description:
Mice were bred on a mixed genetic background of C57BL/6 and 129Sv. Experimental animals were derived from F4 mice of a Pept2+/- line that were mated to yield litters of Pept-/- or Pept2+/+ pups. Kidneys were collected from male animals at the age of 88 (+- 2) days after birth. Mice were killed by cervical dislocation between 8am and 10am to minimise effects of the circadian rhythm on gene expression.
Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). 20ug total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30ul hybridisation buffer (6x SSC, 0,5% SDS 5 fold Denhardt’s solution and 50% formamide) and mixed with 30ul of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre-hybridised microarray, covered with cover slip, placed into a hybridisation chamber (Gene Machines) and immersed in a thermostatic bath at 42C for 18-20 hours.
Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with subtracted background were normalised so that the median of their ratios has became 1.
Keywords = Pept2
Keywords = Slc15a2
Keywords = KO
Keywords = knock-out
Keywords = kidney
Keywords = C57BL/6
Keywords = 129Sv

source_name: RNA pool of 5 right WT mouse kidneys W1-W5

source_name: right kidney of Pept2 KO male mouse K4


title: W1.1


title: Pept2 KO - K3.4

source_name: right kidney of Pept2 KO male mouse K3


title: Pept2 KO - K3.3


title: Pept2 KO - K4.4


title: Pept2 KO - K4.1


title: Pept2 KO - K4.2


title: Pept2 KO - K2.2

source_name: right kidney of Pept2 KO male mouse K2


title: Pept2 KO - K2.3


title: Pept2 KO - K3.2


title: Pept2 KO - K3.1


title: Pept2 KO pool - KOP4

source_name: RNA pool of 5 right Pept2 KO mouse kidneys K1-K5


title: Pept2 KO - K1.2

description:
Mice were bred on a mixed genetic background of C57BL/6 and 129Sv. Experimental animals were derived from F4 mice of a Pept2+/- line that were mated to yield litters of Pept-/- or Pept2+/+ pups. Kidneys were collected from male animals at the age of 88 (+- 2) days after birth. Mice were killed by cervical dislocation between 8am and 10am to minimise effects of the circadian rhythm on gene expression.
Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). 20ug total RNA was used for reverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30ul hybridisation buffer (6x SSC, 0,5% SDS 5 fold Denhardt’s solution and 50% formamide) and mixed with 30ul of reference cDNA solution labelled with the second dye. This hybridisation mixture was placed on a pre-hybridised microarray, covered with cover slip, placed into a hybridisation chamber (Gene Machines) and immersed in a thermostatic bath at 42C for 18-20 hours.
Slides were scanned for both Cy3 and Cy5 with a GenePix 4000A and images were processed by GenePix Pro 3.0. Maen intensities with subtracted background were normalised so that the median of their ratios has became 1.
Keywords = Pept2, Slc15a2, KO, knock-out, kidney, C57BL/6, 129Sv

source_name: right kidney of Pept2 KO male mouse K1


title: Pept2 KO - K1.3


title: Pept2 KO - K1.4


title: Pept2 KO - K1.1


title: Pept2 KO pool - KOP3


title: Pept2 KO pool - KOP1


title: Pept2 KO - K2.1


title: W1.3


title: M7TW01013180

status: Public on Dec 06 2002

description:
Large-scale analysis of the mouse transcriptome.
Dorsal root ganglion
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 356.69  Stdv: 12.12  Min: 341.69  Max: 379.74

hyb_protocol: as per manufacturer's instructions

scan_protocol: as per manufacturer's instructions

source_name: dorsal root ganglion

label_protocol: as per manufacturer's instructions

extract_protocol: as per manufacturer's instructions


title: M7TW01013108

description:
Large-scale analysis of the mouse transcriptome.
Thymus
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 247.27  Stdv: 7.65  Min: 232.18  Max: 260.98

source_name: thymus


title: M7TW01013106

description:
Large-scale analysis of the mouse transcriptome.
Testis
C57BL/6L, male, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 322.51  Stdv: 13.73  Min: 299.24  Max: 349.37

source_name: testis


title: M7TW01013128

description:
Large-scale analysis of the mouse transcriptome.
Ovary
C57BL/6L, female, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 307.75  Stdv: 77.48  Min: 184.03  Max: 424.96

source_name: ovary


title: Pept2 KO pool - KOP2


title: M7TW01013179

description:
Large-scale analysis of the mouse transcriptome.
dorsal root ganglion
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 383.45  Stdv: 15.22  Min: 361.32  Max: 408.85


title: Pept2 KO - K2.4


title: M7TW01013110

description:
Large-scale analysis of the mouse transcriptome.
Trachea
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 313.87  Stdv: 11.93  Min: 285.27  Max: 332.14

source_name: trachea


title: M7TW01013105

description:
Large-scale analysis of the mouse transcriptome.
Testis
C57BL/6L, male, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 230.79  Stdv: 19.43  Min: 200.96  Max: 262.42


title: M7TW01013103

description:
Large-scale analysis of the mouse transcriptome.
Gall bladder
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 403.13  Stdv: 17.80  Min: 379.85  Max: 443.91

source_name: gall bladder


title: M7TW01013102

description:
Large-scale analysis of the mouse transcriptome.
Digits
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 252.86  Stdv: 10.61  Min: 240.37  Max: 272.63

source_name: digits


title: M7TW01013101

description:
Large-scale analysis of the mouse transcriptome.
Digits
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 286.06  Stdv: 8.56  Min: 274.79  Max: 300.96


title: M7TW01013107

description:
Large-scale analysis of the mouse transcriptome.
Thymus
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 255.22  Stdv: 13.71  Min: 226.28  Max: 275.98


title: M7TW01010686

description:
Large-scale analysis of the mouse transcriptome.
Umbilical cord, E18 embryos
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 325.58  Stdv: 14.55  Min: 302.16  Max: 348.55

source_name: umbilical cord


title: M7TW01013109

description:
Large-scale analysis of the mouse transcriptome.
Trachea
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 289.50  Stdv: 6.72  Min: 277.68  Max: 299.19


title: M7TW01010684

description:
Large-scale analysis of the mouse transcriptome.
mammary gland from females with E18 embyros
C57BL/6L, female, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 255.59  Stdv: 10.11  Min: 238.50  Max: 271.99

source_name: mammary gland


title: M7TW01010696

description:
Large-scale analysis of the mouse transcriptome.
Tongue epidermis, dorsal tongue surface
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 287.46  Stdv: 13.90  Min: 265.79  Max: 309.31

source_name: tongue epidermis


title: M7TW01010694

description:
Large-scale analysis of the mouse transcriptome.
Salivary gland
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 295.78  Stdv: 17.52  Min: 268.64  Max: 328.63

source_name: salivary gland


title: M7TW01010695

description:
Large-scale analysis of the mouse transcriptome.
Thyroid
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 326.51  Stdv: 18.02  Min: 297.74  Max: 353.78

source_name: thyroid


title: M7TW01010685

description:
Large-scale analysis of the mouse transcriptome.
Umbilical cord, E18 embryos
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 403.09  Stdv: 17.73  Min: 369.67  Max: 436.25


title: M7TW01010663

description:
Large-scale analysis of the mouse transcriptome.
Bone marrow, flushed from femur
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 285.45  Stdv: 7.90  Min: 273.18  Max: 300.08

source_name: bone marrow


title: M7TW01010638

description:
Large-scale analysis of the mouse transcriptome.
Adrenal gland
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 382.21  Stdv: 20.34  Min: 352.54  Max: 418.36

source_name: adrenal gland


title: M7TW01010699

description:
Large-scale analysis of the mouse transcriptome.
Cortex frontal
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 317.49  Stdv: 10.43  Min: 295.14  Max: 331.45

source_name: cortex frontal


title: M7TW01010673

description:
Large-scale analysis of the mouse transcriptome.
Amygdala
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 240.88  Stdv: 13.00  Min: 216.38  Max: 263.02

source_name: amygdala


title: M7TW01010682

description:
Large-scale analysis of the mouse transcriptome.
Placenta from females with E18 embyros
C57BL/6L, female, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 322.71  Stdv: 17.06  Min: 297.98  Max: 355.16

source_name: placenta


title: M7TW00122050

description:
Large-scale analysis of the mouse transcriptome.
Uterus
C57BL/6L, female, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 362.43  Stdv: 21.44  Min: 335.17  Max: 412.41

source_name: uterus


title: M7TW01010681

description:
Large-scale analysis of the mouse transcriptome.
placenta from females with E18 embryos
C57BL/6L, female, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 313.61  Stdv: 13.16  Min: 292.71  Max: 337.19


title: M7TW00122061

description:
Large-scale analysis of the mouse transcriptome.
Epidermis, dorsal skin without fur
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 282.13  Stdv: 23.65  Min: 251.03  Max: 321.08

source_name: epidermis


title: M7TW00122090

description:
Large-scale analysis of the mouse transcriptome.
Cortex
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 257.91  Stdv: 8.90  Min: 241.50  Max: 274.99

source_name: cortex


title: M7TW00122039

description:
Large-scale analysis of the mouse transcriptome.
Snout epidermis, vibrissa epidermal region
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 268.83  Stdv: 8.11  Min: 255.17  Max: 283.85

source_name: snout epidermis


title: M7TW00122037

description:
Large-scale analysis of the mouse transcriptome.
Adrenal gland
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 213.01  Stdv: 6.47  Min: 202.77  Max: 222.35


title: M7TW00122045

description:
Large-scale analysis of the mouse transcriptome.
Tongue epidermis, dorsal tongue surface
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 427.46  Stdv: 23.58  Min: 375.50  Max: 469.31


title: M7TW00122042

description:
Large-scale analysis of the mouse transcriptome.
Spleen
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 234.60  Stdv: 11.02  Min: 217.07  Max: 253.84

source_name: spleen


title: M7TW00122033

description:
Large-scale analysis of the mouse transcriptome.
salivary gland
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 349.62  Stdv: 10.58  Min: 332.63  Max: 369.11


title: M7TW00122040

description:
Large-scale analysis of the mouse transcriptome.
Snout epidermis, vibrissa epidermal region
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 285.27  Stdv: 8.04  Min: 273.58  Max: 300.96


title: M7TW00122041

description:
Large-scale analysis of the mouse transcriptome.
Spleen
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 403.75  Stdv: 23.28  Min: 362.54  Max: 438.16


title: M7TW00121889

description:
Large-scale analysis of the mouse transcriptome.
Cortex
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 261.21  Stdv: 7.59  Min: 250.89  Max: 279.65


title: M7TW00122013

description:
Large-scale analysis of the mouse transcriptome.
Kidney
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 307.61  Stdv: 20.38  Min: 273.80  Max: 348.81

source_name: kidney


title: M7TW00122047

description:
Large-scale analysis of the mouse transcriptome.
Trigeminal
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 314.26  Stdv: 11.14  Min: 294.15  Max: 332.29

source_name: trigeminal


title: M7TW00122036

description:
Large-scale analysis of the mouse transcriptome.
Skeletal muscle
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 312.31  Stdv: 13.51  Min: 291.96  Max: 338.98

source_name: skeletal muscle


title: M7TW00122074

description:
Large-scale analysis of the mouse transcriptome.
Amygdala
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 268.33  Stdv: 11.64  Min: 249.24  Max: 288.97


title: M7TW00122035

description:
Large-scale analysis of the mouse transcriptome.
Skeletal muscle
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 347.91  Stdv: 14.18  Min: 323.71  Max: 371.58


title: M7TW00121829

description:
Large-scale analysis of the mouse transcriptome.
Prostate
C57BL/6L, male, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 261.78  Stdv: 6.23  Min: 255.49  Max: 277.93

source_name: prostate


title: M7TW00121831

description:
Large-scale analysis of the mouse transcriptome.
Eye
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 267.25  Stdv: 8.85  Min: 253.99  Max: 280.72

source_name: eye


title: M7TW00121824

description:
Large-scale analysis of the mouse transcriptome.
Lymph node, mesenteric
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 284.59  Stdv: 16.72  Min: 260.70  Max: 315.90

source_name: lymph node


title: M7TW00121832

description:
Large-scale analysis of the mouse transcriptome.
Eye
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 272.53  Stdv: 11.06  Min: 256.80  Max: 291.32


title: M7TW00121819

description:
Large-scale analysis of the mouse transcriptome.
Lung
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 250.14  Stdv: 11.39  Min: 234.07  Max: 267.68

source_name: lung


title: M7TW00121827

description:
Large-scale analysis of the mouse transcriptome.
Ovary
C57BL/6L, female, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 205.92  Stdv: 6.06  Min: 196.77  Max: 217.74

source_name: ovary


title: M7TW00121823

description:
Large-scale analysis of the mouse transcriptome.
Lymph node, mesenteric
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 281.71  Stdv: 13.46  Min: 260.68  Max: 305.19


title: M7TW00121822

description:
Large-scale analysis of the mouse transcriptome.
Adipose tissue, mesenteric
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 292.87  Stdv: 7.30  Min: 282.87  Max: 307.11

source_name: adipose tissue


title: M7TW00121804

description:
Large-scale analysis of the mouse transcriptome.
Gall bladder
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 241.90  Stdv: 8.17  Min: 228.80  Max: 256.08

source_name: gall bladder


title: M7TW01010683

description:
Large-scale analysis of the mouse transcriptome.
mammary gland from females with e18 embryos
C57BL/6L, female, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 323.50  Stdv: 10.66  Min: 308.14  Max: 348.71

source_name: mammary gland


title: M7TW00121815

description:
Large-scale analysis of the mouse transcriptome.
Large intestine, cecum
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 248.85  Stdv: 9.03  Min: 234.66  Max: 265.94

source_name: large intestine


title: M7TW00121817

description:
Large-scale analysis of the mouse transcriptome.
Liver
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 229.00  Stdv: 6.41  Min: 216.84  Max: 239.35

source_name: liver


title: M7TW00121814

description:
Large-scale analysis of the mouse transcriptome.
Kidney
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 351.75  Stdv: 15.51  Min: 323.03  Max: 372.32


title: M7TW00121816

description:
Large-scale analysis of the mouse transcriptome.
Large intestine, cecum
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 211.32  Stdv: 7.51  Min: 198.57  Max: 224.94


title: M7TW00121812

description:
Large-scale analysis of the mouse transcriptome.
Hippocampus
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 229.96  Stdv: 6.90  Min: 220.30  Max: 241.73

source_name: hippocampus


title: M7TW00121820

description:
Large-scale analysis of the mouse transcriptome.
Lung
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 271.63  Stdv: 11.08  Min: 254.33  Max: 291.48


title: M7TW00121478

description:
Large-scale analysis of the mouse transcriptome.
Olfactory bulb
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 463.21  Stdv: 16.59  Min: 433.07  Max: 491.87

source_name: olfactory bulb


title: M7TW00121811

description:
Large-scale analysis of the mouse transcriptome.
Hippocampus
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 238.83  Stdv: 11.64  Min: 221.25  Max: 263.09


title: M7TW00121818

description:
Large-scale analysis of the mouse transcriptome.
Liver
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 233.37  Stdv: 7.07  Min: 222.16  Max: 244.82


title: M7TW00121821

description:
Large-scale analysis of the mouse transcriptome.
Adipose tissue, mesenteric
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 226.36  Stdv: 8.71  Min: 213.12  Max: 239.78


title: M7TW00121476

description:
Large-scale analysis of the mouse transcriptome.
Striatum
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 289.86  Stdv: 8.20  Min: 276.78  Max: 301.93

source_name: striatum


title: M7TW00121472

description:
Large-scale analysis of the mouse transcriptome.
Brown fat, interscapular depression
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 275.32  Stdv: 12.26  Min: 259.37  Max: 301.19

source_name: brown fat


title: M7TW00121471

description:
Large-scale analysis of the mouse transcriptome.
Brown fat, interscapular depression
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 254.58  Stdv: 7.52  Min: 242.45  Max: 266.08


title: M7TW00121467

description:
Large-scale analysis of the mouse transcriptome.
Spinal cord, upper half
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 284.53  Stdv: 9.02  Min: 266.71  Max: 299.60

source_name: spinal cord, upper


title: M7TW00121468

description:
Large-scale analysis of the mouse transcriptome.
Spinal cord, upper half
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 237.26  Stdv: 6.00  Min: 227.49  Max: 250.70


title: M7TW00121466

description:
Large-scale analysis of the mouse transcriptome.
Spinal cord, lower half
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 313.08  Stdv: 26.00  Min: 269.95  Max: 353.14

source_name: spinal cord, lower


title: M7TW00121465

description:
Large-scale analysis of the mouse transcriptome.
Spinal cord, lower half
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 254.78  Stdv: 7.36  Min: 243.37  Max: 267.33


title: M7TW00121460

description:
Large-scale analysis of the mouse transcriptome.
Heart
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 295.58  Stdv: 6.26  Min: 285.60  Max: 304.11

source_name: heart


title: M7TW00121369

description:
Large-scale analysis of the mouse transcriptome.
Bone, femur
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 305.99  Stdv: 11.83  Min: 288.42  Max: 329.29

source_name: bone


title: M7TW00121370

description:
Large-scale analysis of the mouse transcriptome.
Bone, femur
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 226.71  Stdv: 4.69  Min: 220.80  Max: 237.19


title: M7TW00121357

description:
Large-scale analysis of the mouse transcriptome.
Hypothalamus
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 258.13  Stdv: 7.82  Min: 246.78  Max: 280.71

source_name: hypothalamus


title: M7TW00121359

description:
Large-scale analysis of the mouse transcriptome.
Heart
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 263.13  Stdv: 7.97  Min: 250.68  Max: 278.01


title: M7TW00121354

description:
Large-scale analysis of the mouse transcriptome.
Small intestine, duodenum
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 269.23  Stdv: 8.45  Min: 259.01  Max: 286.06

source_name: small intestine


title: M7TW00121388

description:
Large-scale analysis of the mouse transcriptome.
Cerebellum
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 277.60  Stdv: 15.79  Min: 256.68  Max: 315.91

source_name: cerebellum


title: M7TW00121355

description:
Large-scale analysis of the mouse transcriptome.
Stomach
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 218.04  Stdv: 7.29  Min: 206.42  Max: 231.90

source_name: stomach


title: M7TW00121387

description:
Large-scale analysis of the mouse transcriptome.
Cerebellum
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 251.51  Stdv: 10.45  Min: 237.31  Max: 274.78


title: M7TW00121353

description:
Large-scale analysis of the mouse transcriptome.
Small intestine, duodenum
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 241.08  Stdv: 6.20  Min: 230.91  Max: 251.39


title: M7TW00122048

description:
Large-scale analysis of the mouse transcriptome.
Trigeminal
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 342.14  Stdv: 12.32  Min: 321.12  Max: 362.82

source_name: trigeminal


title: M7TW00122049

description:
Large-scale analysis of the mouse transcriptome.
Uterus
C57BL/6L, female, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 272.79  Stdv: 45.66  Min: 201.48  Max: 334.55

source_name: uterus


title: M7TW00121830

description:
Large-scale analysis of the mouse transcriptome.
prostate
C57BL/6L, male, 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 269.71  Stdv: 12.29  Min: 252.68  Max: 290.32

source_name: prostate


title: M7TW01010664

description:
Large-scale analysis of the mouse transcriptome.
Bone marrow, flushed from femur
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 343.37  Stdv: 18.12  Min: 316.93  Max: 370.52

source_name: bone marrow


title: M7TW00121852

description:
Large-scale analysis of the mouse transcriptome.
Bladder
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 447.07  Stdv: 22.40  Min: 408.35  Max: 493.15

source_name: bladder


title: M7TW00121475

description:
Large-scale analysis of the mouse transcriptome.
Striatum
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 239.34  Stdv: 8.95  Min: 229.80  Max: 259.97


title: M7TW00121458

description:
Large-scale analysis of the mouse transcriptome.
Hypothalamus
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 329.47  Stdv: 7.51  Min: 319.02  Max: 343.31


title: M7TW00121851

description:
Large-scale analysis of the mouse transcriptome.
Bladder
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 342.12  Stdv: 18.37  Min: 313.81  Max: 371.22


title: M7TW00122062

description:
Large-scale analysis of the mouse transcriptome.
Epidermis, dorsal skin without fur
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 362.52  Stdv: 21.48  Min: 334.00  Max: 406.09

source_name: epidermis


title: M7TW00121356

description:
Large-scale analysis of the mouse transcriptome.
Stomach
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 240.76  Stdv: 8.41  Min: 228.93  Max: 253.64


title: M7TW00122043

description:
Large-scale analysis of the mouse transcriptome.
Thyroid
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 325.24  Stdv: 8.85  Min: 311.13  Max: 340.74

source_name: thyroid


title: M7TW00121391

description:
Large-scale analysis of the mouse transcriptome.
Cortex frontal
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 317.49  Stdv: 10.43  Min: 295.14  Max: 331.45

source_name: cortex frontal


title: M7TW00121477

description:
Large-scale analysis of the mouse transcriptome.
Olfactory bulb
C57BL/6L, M/F pool (4 males, 3 females), 8-11 weeks
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 277.21  Stdv: 10.95  Min: 261.91  Max: 295.99

source_name: olfactory bulb


title: P-S1500, biological rep2

status: Public on Dec 19 2006

city: Yokohama

first: Akiko

last: Maruyama-Nakashita

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Plant Science Center

description: Gene expression data from root of PSULTR1;2-GFP plants vertically grown for 10 days on S1500 medium.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene Array Scanner (Agilent Technologies, Palo Alto, CA).

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

label: biotin

organism: Arabidopsis thaliana

source_name: Roots of PSULTR1;2-GFP plants

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis plants (Col-0) were grown at 22C under 16 h/8 h light and dark cycles for 10 days. Plants were grown on mineral nutrient media (Hirai et al. 1995 Plant Cell Physiology 36: 1331) containing 1% sucrose, 0.8% agar. For preparation of agar medium, agar was washed twice with 1 L of de-ionized water and vacuum filtrated. The agar medium with complete replacement of MgSO4 to MgCl2 contained approximately 10 µM of residual sulfate derived from agar. The S1500 agar media were prepared by adding 1500 µM of MgSO4.

extract_protocol: Total RNA was prepared using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Root samples were transferred to liquid nitrogen before RNA extraction.

tag: Arabidopsis thaliana cv. Columbia transformed with the T-DNA construct of pBI101 harbouring promoter region of SULTR1;2 fused to GFP (PSULTR1;2-GFP plants; Maruyama-Nakashita et al. 2004 Plant Journal 38

tag: Tissue

value: roots


title: earlybird wildtype hippocampus hew2 B

status: Public on Dec 15 2006

city: Philadelphia

first: Maja

last: Bucan

state: PA

address: 415 Curie Blvd

institute: UPENN

description: hippocampus from wild type littermate of earlybird mutant mouse

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: hippocampus

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 50 mg of tissue was homogenized in 1 ml TriZol reagent and total RNA was extracted according to manufacture's protocol. Total RNA was cleaned up using an RNeasy kit (Qiagen).

tag: earlybird wildtype hippocampus


title: large airways, smoker 010615R, MAS5

status: Public on Nov 21 2006

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: large airways, non-smoker 010615R, MAS5

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HuGeneFL. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray 2500.

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

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA.

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: M

tag: Ethnic group

value: white

tag: Smoking Status

value: smoker, 24 pack-years

tag: Lung

value: right