title: rdi1∆ mutant vs Wild-type in macrophage co-culture

status: Public on May 28 2009

city: Lynchburg

middle: S

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

description: Gene expression was compared between WT and rdi1∆ mutant strains of C. neoformans grown in concert with macrophages in tissue culture medium.

hyb_protocol: Hybridization was performed at the Duke University Microarray Facility following the Hybridization protocol (http://microarray.genome.duke.edu/).

scan_protocol: Slides were scanned at the Duke University Microarray Facility using an Axon Genepix  4000B scanner (http://microarray.genome.duke.edu/).

data_processing: Extracted data were imported into a statistical software package (JMP Genomics v3.0, SAS Institute, Cary, NC).  Mixed model analysis of microarray data (Wolfinger et al., 2001) was implemented to evaluate gene expression differences using statistical approaches described elsewhere (Chhabra, et al., 2003; Pysz et al., 2004; Price et al., 2005).  Briefly, data was imported into JMP Genomics using the Genepix Import engine.  Initial data quality was assessed using kernel density plots and boxplots output from the Data Distribution process.  The data was normalized using the ANOVA Normalization process, with fixed effects channel and treatment, and array treated as a random effect.  Variation due to treatment was retained during normalization.  Following a post-normalization assessment of data quality using output from Data Distribution, the normalized data was subjected to gene-by-gene modeling using the ANOVA process.  Once again, fixed effects (channel and treatment) were estimated and variation due to the random effect (array) was removed for each gene.  Least squares estimates of gene-specific treatment effects for wild-type and mutant genotypes were obtained for each gene.  The difference between treatment effects for both genotypes can be loosely considered as log2-transformed fold changes (Wolfinger et al., 2001).  Genes were considered differentially expressed if they possessed p-values less than α.  The value of α (0.000573) was chosen based on the significance of the difference of RDI1 expression between genotypes.

label: Cy3 or Cy5; dye swap experiments were performed

organism: Cryptococcus neoformans H99

source_name: Wild-type in macrophage co-culture

label_protocol: Labeling was performed at the Duke University Microarray Facility following the Direct Labeling protocol for spotted arrays (http://microarray.genome.duke.edu/).

extract_protocol: RNA was prepared using the Qiagen RNeasy Plant Mini kit (Qiagen Inc., Valencia, CA).  using manufacturer's instructions for Plants & Fungi.

tag: C. neoformans H99 was coincubated with J774A.1 macrophages at a ratio of 10:1 (yeast:macrophage).  Cultures were incubated at 37°C, 5% CO2 for 1hour.

source_name: rdi1∆ mutant in macrophage co-culture

tag: C. neoformans MPC3 (rdi1∆::nat) was coincubated with J774A.1 macrophages at a ratio of 10:1 (yeast:macrophage).  Cultures were incubated at 37°C, 5% CO2 for 1hour.


title: Rec8-FLAG distribution on chromosome III-V at meiosis 5 hr

status: Public on May 29 2009

type: genomic

city: Kisarazu

first: Kazuto

last: Kugou

state: Chiba

address: 2-6-7 KazusaKamatatri

department: Department of Frontier Research

country: Japan

institute: Kazusa DNA Research Institute

description:
ChIP-chip data used for the mapping of Rec8 distribution on chromosome III-V at meiosis 5 hr
Used baseline: WCE fraction (REC8-FLAG cells at meiosis 2 hr, chromosome III-V)

hyb_protocol: Following denaturation at 100 C for 10 minutes, cooling, and spin-down, 200 micro liter of hybridization mixuter was hybridized for 16 hours at 42 C on GeneChip SC3456a520015F using hybridization oven 640 (affymetrix). Each hybridization mixture contains the end-labbeled DNA, 6xSSPE, 0.005% Triton X-100, 0.1 mg/ml herring sperm DNA, oligo B2 (affymetrix) and hybridization control (affymetrix).

scan_protocol: Washing and scanning protocol (EukGE-WS1v3) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix). Arrays were scanned by Hewlett-Packard GeneArray Scanner at an emission wavelength of 560 nm at 7.5 microM resolution.

data_processing:
Data analyses were performed as previously described in Methods in Enzymology, Elsevier Life Sciences (CA), vol.409,chapter 23,389-410 in “DNA Repair” (edited by J.Campbell) (2006).
Primary data analyses were carried out with GeneChip Operating Software (GCOS 1.4) using default settings to obtain signal and detection p-value.
To discriminate significant signals for binding to DNA, signals from the ChIP fraction scan were compared to the WCE fraction scan with GCOS 1.4 using default settings.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Chromatin-immunoprecipitated DNA

label_protocol: End labeling by terminal transferase

growth_protocol: Cells were grown on a YPD plate for 2 days at 30C. The cells were grown to a density of 4.0x10e7 cells/ml at 30C in SPS presporulation medium (0.5% yeast extract, 1% peptone, 0.17% yeast nitrogen base w/o amino acid and ammonium sulfate, 1% potassium acetate, 0.5% ammonium sulfate, usual level of amino acids, 50 mM potassium phthalate buffer pH 5.0, and antifoam). The cells were suspended in sporulation medium (1% potasium acetate, 1/5 level of amino acids, and polypropylene glycol) to a density of 2x10e7 cells/ml, and incubated at 30C for sporulation.

extract_protocol:
The cells were disrupted using Multi-Beads Shocker (YASUI KIKAI, Osaka) with 0.5-mm zirconia beads. Whole cell extract was sonicated to obtain average 500 bp genomic DNA fragments.
The WCE was immunoprecipitated with anti-FLAG monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) coupled to Dynabeads (Invitrogen, protein A Dynabeads).
The chromatin immunoprecipitated sample was incubated overnight at 65ºC, incubated with proteinase K, extracted with phenol/chloroform/isoamylalcohol, precipitated, and resuspended in TE and incubated with RNaseA.
The DNA was amplified by PCR after random priming as previously described (Katou et al., 2003, nature). The amplified DNA was digested with Dnase I to a mean size of 100 bp. After DNase I inactivation at 95ºC, fragments were labelled with indicated label protocol.

treatment_protocol:
100 ml culture (2x10e9 cells) was taken at 5 hrs in sporulation medium.
The culture was fixed in 1% formaldehyde for 10 min at room temperature and then treated with 125 mM glycine for 5 min at room temperature. The cells were washed with 40 ml of ice-cold TBS twice, freezed with liquid nitrogen, and stored at -80C.

tag: SK1 background strain expressing FLAG tagged Rec8 protein

tag: Strain

tag: Culture

value: 5 hrs after transfer to sporulation medium


title: Spo11-FLAG distribution on chromosome III-V at meiosis 1.5 hr

description:
ChIP-chip data used for the mapping of Spo11 distribution on chromosome III-V at meiosis 1.5 hr
Used baseline: WCE fraction (SPO11-FLAG cells at meiosis 4 hr, chromosome III-V)

treatment_protocol:
100 ml culture (2x10e9 cells) was taken at 1.5 hrs in sporulation medium.
The culture was fixed in 1% formaldehyde for 10 min at room temperature and then treated with 125 mM glycine for 5 min at room temperature. The cells were washed with 40 ml of ice-cold TBS twice, freezed with liquid nitrogen, and stored at -80C.

tag: SK1 background strain expressing FLAG tagged Spo11 protein

value: 1.5 hrs after transfer to sporulation medium


title: NaCl1_rpd3_60 min

status: Public on May 21 2009

type: RNA

city: Madison

first: Audrey

middle: P.

last: Gasch

state: WI

address: 425-g Henry Mall

department: Laboratory of Genetics

country: USA

institute: University of Wisconsin Madison

description: Comparison of rpd3  before and after addition of NaCl to 0.7M in YPD - replicate #1

hyb_protocol: As indicated in Gasch AP Methods in Enzymology 350: 393-414  To prepare the probe for hybridization to a ~22 x 22 mm microarray, combine 5/zl of each of the Cy-dUTP labeled samples or 10/zl of the combined aminoallyllabeled sample, 1/zl of 10 mg/ml poly(A) carrier (Sigma), 2.3/zl 20× SSC, and 0.36 tzl 10% SDS for a final volume of 14/zl (if the microarray is larger than 22 x 22 mm add to the 10 #1 of probe solution 2.6 #1 poly(A), 5.0 20x SSC, and 0.78 #1 10% SSD and adjust the final volume to 30 #1 with water). Denature the probe by heating at 94 ° for 3 min, then cool to room temperature by rapidly transferring to a microfuge and spinning for 10 sec (avoid adding bubbles during handling). Do not chill the probe on ice as salt will precipitate from the solution. Prepare the hybridization chamber (Coming): place the microarray into the chamber and add ~20/zl 3× SSC to each of the hybridization wells in the chamber and an additional -~30/zl of 3x SSC divided into isolated drops on the edges of the microarray. Insufficient volume will result in inadequate chamber hydration during hybridization, causing the probe to dry out under the coverslip. Select multiple microscope slide coverslips of the appropriate size (Coming) that appear free of dust, chips, and scratches, and prop them for easy access with a tweezers. Adding the probe to the microarray and sealing with the coverslip requires some experience and personal technique. It is advisable to practice the following procedure before hand. To the center of the microarray, deposit 12-15/zl of the denatured and cooled probe for 22 x 22 mm arrays, or 28-30 #1 probe for 22 x 44 mm microarrays. Bubbles can prevent proper hybridization, and therefore they should be avoided and removed when possible. Large bubbles can be popped with the comer of a coverslip, but great care should be taken not to touch the microarray surface. Quickly place the coverslip directly over the deposited probe and gently drop or place the coverslip over the array. The coverslip should not be moved so as to prevent scratching of the microarray surface; however, in unavoidable cases it can be gently positioned by sliding. Close the hybridization chamber and gently and quickly submerge the chamber in a 65 ° water bath. For optimal signal, hybridize the arrays for 7-16 hr. For consistent results, the hybridization conditions, including hybridization time, should be maintained for all microarrays.

scan_protocol: Arrays were scanned on an Axon 4000B scanner

data_processing: Data were extracted using GenePix 6.0.  Data were normalized by regional mean-centering as described by Lyne et al. 2003 BMC Genomics

label: Oyster 550 cyanine dye

molecule: total RNA

source_name: BYrpd3 grown in YPD at 30C (time 0 reference)

label_protocol: Indirect labeling using amino-allyl-dUTP and cyanine dyes from Flownamics (Madison, Wi) as described in Gasch AP Methods in Enzymology 350: 393-414

growth_protocol: Unless otherwise noted, cells were grown 3 doublings in YPD or specified medium at 30C to OD600 ~0.5

extract_protocol: Hot-phenol RNA extraction as described in Gasch AP Methods in Enzymology 350: 393-414

treatment_protocol: Stresses were added directly to the culture at the indicated concentrations.  For heat shock experiments, cells were collected by rapid filtration at 25C and resuspended in fresh YPD heated to 37C.  For reverse heat shock experiments, cells were grown 3 doublings in YPD at 37C, collected by brief centrifugation, and resuspended in fresh YPD at 25C

tag: Strain BY4741-rpd3:KanMX (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpd3::KanMX)

label: Oyster cyanine 650 dye

source_name: BYrpd3 60 min after addition of NaCl to 0.75M


title: Spo11-FLAG distribution on chromosome III-V at meiosis 2 hr

description:
ChIP-chip data used for the mapping of Spo11 distribution on chromosome III-V at meiosis 2 hr
Used baseline: WCE fraction (SPO11-FLAG cells at meiosis 4 hr, chromosome III-V)

treatment_protocol:
100 ml culture (2x10e9 cells) was taken at 2 hrs in sporulation medium.
The culture was fixed in 1% formaldehyde for 10 min at room temperature and then treated with 125 mM glycine for 5 min at room temperature. The cells were washed with 40 ml of ice-cold TBS twice, freezed with liquid nitrogen, and stored at -80C.

value: 2 hrs after transfer to sporulation medium


title: NaCl1_rpd3_30 min

source_name: BYrpd3 30 min after addition of NaCl to 0.75M


title: NaCl1_rpd3_90 min

source_name: BYrpd3 90 min after addition of NaCl to 0.75M


title: RH_1_wt_20 min

description: Comparison of wt before and after reciprocal heat shock from 37C to 25C.  Cells grown ~3 generations in YPD at 37C before centrifugation and resuspension in fresh YPD at 25C - replicate #1

source_name: BY4741 grown at 37C (time 0 reference)

tag: Strain BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)

source_name: BY4741 20 min after shift to 25C YPD


title: RH_1_wt_40 min

source_name: BY4741 40 min after shift to 25C YPD


title: RH_1_wt_5 min

source_name: BY4741 5 min after shift to 25C YPD


title: RH_1_rpd3_40 min

description: Comparison of rpd3 before and after reciprocal heat shock from 37C to 25C.  Cells grown ~3 generations in YPD at 37C before centrifugation and resuspension in fresh YPD at 25C - replicate #2

source_name: BYrpd3 grown at 37C (time 0 reference)

source_name: BYrpd3 40 min after shift to 25C YPD


title: NaCl1_rpd3_15 min

source_name: BYrpd3 15 min after addition of NaCl to 0.75M


title: NaCl1_wt_60 min

description: Comparison of wt before and after addition of NaCl to 0.7M in YPD - replicate #1

source_name: BY4741 grown in YPD at 30C (time 0 reference)

source_name: BY4741 60 min after addition of NaCl to 0.75M


title: NaCl1_wt_30 min

source_name: BY4741 30 min after addition of NaCl to 0.75M


title: H2O2_30min_msn2/msn4/rpd3-1

description: Comparison of msn2/msn4/rpd3 before and 30 min after addition of 0.4 mM H2O2 - replicate #1

source_name: BYmsn2/msn4/rpd3 grown at 30C (time 0 reference) #1

tag: Strain BY4741-msn2:KanMX/msn4::URA3/rpd3::LEU2 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 msn2::KanMX msn4::URA3 rpd3::LEU2)

source_name: BYmsn2/msn4/rpd3 30 min after addition of 0.4 mM H2O2 #1


title: H2O2_30min_RMY491(H4KQ)-3

description: Comparison of RMY491 (H4KQ) grown in SC-Trp before and 30 min after 0.4mM H2O2 - replicate #3

source_name: RMY491 (H4KQ mutant) 30 min after addition of 0.4 mM H2O2 #3

tag: MATα ura3-52 leu2-3,112 trp1-289 his3Δ1 Δ(hht1-hhf1)(hht2-hhf2) pNS329 [CEN ARS TRP1 HHT1-hhf1-10 H4(K5,8,12,16Q]

source_name: RMY491 (H4KQ mutant) grown at 30C in SC-Trp (time 0 reference) #3


title: H2O2_30min_msn2/msn4/rpd3-2

description: Comparison of msn2/msn4/rpd3 before and 30 min after addition of 0.4 mM H2O2 - replicate #2

source_name: BYmsn2/msn4/rpd3 grown at 30C (time 0 reference) #2

source_name: BYmsn2/msn4/rpd3 30 min after addition of 0.4 mM H2O2 #2


title: H2O2_30min_msn2/msn4/rpd3-3

description: Comparison of msn2/msn4/rpd3 before and 30 min after addition of 0.4 mM H2O2 - replicate #3

source_name: BYmsn2/msn4/rpd3 30 min after addition of 0.4 mM H2O2 #3

source_name: BYmsn2/msn4/rpd3 grown at 30C (time 0 reference) #3


title: H2O2_30min_msn2/msn4-2

description: Comparison of msn2/msn4 before and 30 min after addition of 0.4 mM H2O2 - replicate #2

source_name: BYmsn2/msn4 grown at 30C (time 0 reference) #2

tag: Strain BY4741-msn2:KanMX/msn4::URA3 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 msn2::KanMX msn4::URA3)

source_name: BYmsn2/msn4 30 min after addition of 0.4 mM H2O2 #2


title: NaCl1_wt_15 min

source_name: BY4741 15 min after addition of NaCl to 0.75M


title: H2O2_30min_msn2/msn4-3

description: Comparison of msn2/msn4 before and 30 min after addition of 0.4 mM H2O2 - replicate #3

source_name: BYmsn2/msn4 grown at 30C (time 0 reference) #3

source_name: BYmsn2/msn4 30 min after addition of 0.4 mM H2O2 #3


title: H2O2_30min_msn2/msn4-1

description: Comparison of msn2/msn4 before and 30 min after addition of 0.4 mM H2O2 - replicate #1

source_name: BYmsn2/msn4 grown at 30C (time 0 reference) #1

source_name: BYmsn2/msn4 30 min after addition of 0.4 mM H2O2 #1


title: H2O2_30min_rpd3+pRS-rpd3H150:151A

description: Comparison of rpd3 strain harboring catalytically inactive rpd3 before and 30 min after 0.4 mM H2O2

source_name: BYrpd3 + pRS-rpd3H150:151A plasmid 30 min after addition of 0.4 mM H2O2

source_name: BYrpd3 + pRS-rpd3H150:151A plasmid grown in Sc-Leu at 30C


title: H2O2_30min_rpd3+pRS-RPD3

description: Comparison of rpd3 strain complemented with pRS-RPD3 before and 30 min after 0.4 mM H2O2

source_name: BYrpd3 + pRS-RPD3 plasmid 30 min after addition of 0.4 mM H2O2

source_name: BYrpd3 + pRS-RPD3 plasmid grown in SC-Leu at 30C


title: H2O2_30min_RMY491(H4KQ)-2

description: Comparison of RMY491 (H4KQ) grown in SC-Trp before and 30 min after 0.4mM H2O2 - replicate #2

source_name: RMY491 (H4KQ mutant) grown at 30C in SC-Trp (time 0 reference) #2

source_name: RMY491 (H4KQ mutant) 30 min after addition of 0.4 mM H2O2 #2


title: H2O2_30min_NSY429(wt)-1

description: Comparison of NSY429 (wt) grown in SC-Trp before and 30 min after 0.4mM H2O2 - replicate #1

source_name: NSY429 (wt) grown at 30C in SC-Trp (time 0 reference) #1

tag: MATα ura3-52 leu2-3,112 trp1-289 his3Δ1 Δ(hht1-hhf1)(hht2-hhf2) pNS329 [CEN ARS TRP1 HHT1-HHF1]

source_name: NSY429 (wt) 30 min after addition of 0.4 mM H2O2 #1


title: H2O2_30min_NSY429(wt)-3

description: Comparison of NSY429 (wt) grown in SC-Trp before and 30 min after 0.4mM H2O2 - replicate #3

source_name: NSY429 (wt) 30 min after addition of 0.4 mM H2O2 #3

source_name: NSY429 (wt) grown at 30C in SC-Trp (time 0 reference) #3


title: H2O2_30min_NSY429(wt)-2

description: Comparison of NSY429 (wt) grown in SC-Trp before and 30 min after 0.4mM H2O2 - replicate #2

source_name: NSY429 (wt) grown at 30C in SC-Trp (time 0 reference) #2

source_name: NSY429 (wt) 30 min after addition of 0.4 mM H2O2 #2


title: H2O2_30min_RMY491(H4KQ)-1

description: Comparison of RMY491 (H4KQ) grown in SC-Trp before and 30 min after 0.4mM H2O2 - replicate #1

source_name: RMY491 (H4KQ mutant) grown at 30C in SC-Trp (time 0 reference) #1

source_name: RMY491 (H4KQ mutant) 30 min after addition of 0.4 mM H2O2 #1


title: H2O2_30min_ume6-4

description: Comparison of ume6 before and 30 min after 0.4 mM H2O2 - replicate #4

source_name: BYume6 grown at 30C (time 0 reference) #4

tag: Strain BY4741-ume6:KanMX (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 ume6::KanMX)

source_name: BYume6 30 min after addition of 0.4 mM H2O2 #4


title: NaCl1_wt_90 min

source_name: BY4741 grown in YPD at 30C (time 0 reference)

source_name: BY4741 90 min after addition of NaCl to 0.75M


title: H2O2_30min_ume6-3

description: Comparison of ume6 before and 30 min after 0.4 mM H2O2 - replicate #3

source_name: BYume6 grown at 30C (time 0 reference) #3

source_name: BYume6 30 min after addition of 0.4 mM H2O2 #3


title: H2O2_30min_ume6-1

description: Comparison of ume6 before and 30 min after 0.4 mM H2O2 - replicate #1

source_name: BYume6 grown at 30C (time 0 reference) #1

source_name: BYume6 30 min after addition of 0.4 mM H2O2 #1


title: H2O2_30min_rco1-2

description: Comparison of rco1 before and 30 min after 0.4 mM H2O2 - replicate #2

source_name: BYrco1 grown at 30C in YPD (time 0 reference) #2

tag: Strain BY4741-rco1:KanMX (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rco1::KanMX)

source_name: BYrco1 30 min after addition of 0.4 mM H2O2 #2


title: H2O2-1_rco1_40 min

description: Comparison of rco1 before and after 0.4 mM H2O2

source_name: BYrco1 grown at 30C in YPD (time 0 reference)

source_name: BYrco1 40 min after addition of 0.4 mM H2O5


title: H2O2_30min_rco1-3

description: Comparison of rco1 before and 30 min after 0.4 mM H2O2 - replicate #3

source_name: BYrco1 30 min after addition of 0.4 mM H2O2 #3

source_name: BYrco1 grown at 30C in YPD (time 0 reference) #3


title: H2O2-1_rco1_60 min

source_name: BYrco1 60 min after addition of 0.4 mM H2O6


title: H2O2-1_rco1_30 min

source_name: BYrco1 30 min after addition of 0.4 mM H2O4


title: H2O2-1_pho23_40 min

description: Comparison of pho23 before and after 0.4 mM H2O2

source_name: BYpho23 grown at 30C in YPD (time 0 reference)

tag: Strain BY4741-pho23:KanMX (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 pho3::KanMX)

source_name: BYpho23 40 min after addition of 0.4 mM H2O5


title: H2O2_30min_pho23-2

description: Comparison of pho23 before and 30 min after 0.4 mM H2O2 - replicate #3

source_name: BYpho23 grown at 30C in YPD (time 0 reference) #2

source_name: BYpho23 30 min after addition of 0.4 mM H2O2 #2


title: H2O2-1_rpd3_40 min

description: Comparison of rpd3 before and after addition of 0.4 mM H2O2

source_name: BYrpd3 40 min after addition of 0.4 mM H2O5

source_name: BYrpd3 grown in YPD at 30C (time 0 reference)


title: H2O2-1_rpd3_30 min

source_name: BYrpd3 30 min after addition of 0.4 mM H2O4


title: H2O2-1_pho23_60 min

source_name: BYpho23 60 min after addition of 0.4 mM H2O6


title: H2O2_30min_pho23-3

description: Comparison of pho23 before and 30 min after addition of 0.4 mM H2O2 - replicate #6

source_name: BYpho23 grown at 30C in YPD (time 0 reference) #3

source_name: BYpho23 30 min after addition of 0.4 mM H2O2 #3


title: H2O2-1_rco1_10 min

source_name: BYrco1 10 min after addition of 0.4 mM H2O2


title: H2O2-1_pho23_30 min

source_name: BYpho23 30 min after addition of 0.4 mM H2O4


title: H2O2-1_rpd3_60 min

source_name: BYrpd3 60 min after addition of 0.4 mM H2O6


title: H2O2-1_pho23_20 min

source_name: BYpho23 20 min after addition of 0.4 mM H2O3


title: H2O2-1_rco1_20 min

source_name: BYrco1 grown at 30C in YPD (time 0 reference)

source_name: BYrco1 20 min after addition of 0.4 mM H2O3


title: H2O2_30min_rpd3-2

description: Comparison of rpd3 before and 30 min after 0.4mM H2O2 - replicate #2

source_name: BYrpd3 30 min after addition of 0.4 mM H2O2 #2

source_name: BYrpd3 grown at 30C (time 0 reference) #2


title: H2O2-1_pho23_10 min

source_name: BYpho23 grown at 30C in YPD (time 0 reference)

source_name: BYpho23 10 min after addition of 0.4 mM H2O2


title: H2O2_30min_rpd3-3

description: Comparison of rpd3 before and 30 min after 0.4mM H2O2 - replicate #3

source_name: BYrpd3 grown at 30C (time 0 reference) #3

source_name: BYrpd3 30 min after addition of 0.4 mM H2O2 #3


title: H2O2_30min_ume6-2

description: Comparison of ume6 before and 30 min after 0.4 mM H2O2 - replicate #2

source_name: BYume6 grown at 30C (time 0 reference) #2

source_name: BYume6 30 min after addition of 0.4 mM H2O2 #2


title: H2O2_30min_wt-4

description: Comparison of wt before and 30 min after 0.4mM H2O2 - replicate #4

source_name: BY4741 grown at 30C (time 0 reference) #4

source_name: BY4741 30 min after addition of 0.4 mM H2O2 #4


title: H2O2_30min_wt-6

description: Comparison of wt before and 30 min after 0.4mM H2O2 - replicate #6

source_name: BY4741 grown at 30C (time 0 reference) #6

source_name: BY4741 30 min after addition of 0.4 mM H2O2 #6


title: H2O2_30min_wt-8

description: Comparison of wt before and 30 min after 0.4mM H2O2 - replicate #8

source_name: BY4741 grown at 30C (time 0 reference) #8

source_name: BY4741 30 min after addition of 0.4 mM H2O2 #8


title: H2O2_30min_wt-3

description: Comparison of wt before and 30 min after 0.4mM H2O2 - replicate #3

source_name: BY4741 grown at 30C (time 0 reference) #3

source_name: BY4741 30 min after addition of 0.4 mM H2O2 #3


title: H2O2-1_rpd3_10 min

source_name: BYrpd3 10 min after addition of 0.4 mM H2O2

source_name: BYrpd3 grown in YPD at 30C (time 0 reference)


title: H2O2-1_rpd3_20 min

source_name: BYrpd3 20 min after addition of 0.4 mM H2O3


title: H2O2_30min_wt-7

description: Comparison of wt before and 30 min after 0.4mM H2O2 - replicate #7

source_name: BY4741 grown at 30C (time 0 reference) #7

source_name: BY4741 30 min after addition of 0.4 mM H2O2 #7


title: H2O2_30min_wt-2

description: Comparison of wt before and 30 min after 0.4mM H2O2 - replicate #2

source_name: BY4741 30 min after addition of 0.4 mM H2O2 #2

source_name: BY4741 grown at 30C (time 0 reference) #2


title: H2O2_30min_wt-5

description: Comparison of wt before and 30 min after 0.4mM H2O2 - replicate #5

source_name: BY4741 grown at 30C (time 0 reference) #5

source_name: BY4741 30 min after addition of 0.4 mM H2O2 #5


title: H2O2-1_wt_60 min

description: Comparison of wt before and after addition of 0.4 mM H2O2

source_name: BY4147 60 min after addition of 0.4 mM H2O6

source_name: BY4741 grown in YPD at 30C (time 0 reference)


title: H2O2-1_wt_40 min

source_name: BY4147 40 min after addition of 0.4 mM H2O5


title: H2O2-1_wt_20 min

source_name: BY4147 20 min after addition of 0.4 mM H2O3


title: H2O2-1_wt_30 min

source_name: BY4147 30 min after addition of 0.4 mM H2O4


title: H2O2-1_wt_10 min

source_name: BY4147 10 min after addition of 0.4 mM H2O2


title: HS3_wt+TSA_5 min

description: Comparison of wt + DMSO/TrichostatinA control before and after 25C to 37C heat shock

source_name: BY4741 grown in YPD at 25C + DMSO + 10 uM TSA  - 5 min after shift to 37C YPD + DMSO + 10 uM TSA

source_name: BY4741 grown in YPD at 25C + DMSO + 10 uM TSA for 15 min (time 0 reference)


title: HS3_wt+TSA_30 min

source_name: BY4741 grown in YPD at 25C + DMSO + 10 uM TSA  - 30 min after shift to 37C YPD + DMSO + 10 uM TSA


title: HS3_wt+DMSO_15 min

description: Comparison of wt + DMSO control before and after 25C to 37C heat shock

source_name: BY4741 grown in YPD at 25C + DMSO  - 15 min after shift to 37C YPD + DMSO

source_name: BY4741 grown in YPD at 25C + DMSO for 15 min (time 0 reference)


title: HS_20min_rpd3+pRS-RPD3

description: Comparison of rpd3 strain complemented with pRS-RPD3 before and 20 min after 25C to 37C heat shock

source_name: BYrpd3 + pRS-RPD3 plasmid 20 min after shift to 37C

source_name: BYrpd3 + pRS-RPD3 plasmid grown in SC-Leu at 25C


title: HS_20min_rpd3+pRS-rpd3H150:151A

description: Comparison of rpd3 strain harboring catalytically inactive rpd3 before and 20 min after 25C to 37C heat shock

source_name: BYrpd3 + pRS-rpd3H150:151A plasmid 20 min after shift to 37C

source_name: BYrpd3 + pRS-rpd3H150:151A plasmid grown in SC-Leu at 25C


title: HS3_wt+TSA_15 min

source_name: BY4741 grown in YPD at 25C + DMSO + 10 uM TSA  - 15 min after shift to 37C YPD + DMSO + 10 uM TSA


title: HS3_wt+DMSO_30 min

source_name: BY4741 grown in YPD at 25C + DMSO  - 30 min after shift to 37C YPD + DMSO


title: HS3_wt+DMSO_5 min

source_name: BY4741 grown in YPD at 25C + DMSO  - 5 min after shift to 37C YPD + DMSO


title: HS_20min_rpd3+pRS415

description: Comparison of rpd3 strain with pRS415 before and 20 min after 25C to 37C heat shock

source_name: BYrpd3 + pRS-415 plasmid 20 min after shift to 37C

source_name: BYrpd3 + pRS-415 plasmid grown in SC-Leu at 25C


title: HS2_wt_60 min

description: Comparison of WT before and after 25C to 37C heat shock - replicate #1

source_name: BY4741 grown in YPD at 25C (time 0 reference)

source_name: BY4741 60 min after shift to 37C in YPD


title: HS1_rpd3_5 min

description: Comparison of rpd3 before and after heat shock from 25C to 37C - replicate #1

source_name: BYrpd3 grown in YPD at 25C (time 0 reference)

source_name: BYrpd3  5 min after shift to 37C in YPD


title: HS2_wt_5 min

source_name: BY4741 5 min after shift to 37C in YPD


title: HS2_rpd3_20 min

description: Comparison of rpd3 before and after 25C to 37C heat shock - replicate #2

source_name: BYrpd3 grown in YPD at 30C (time 0 reference)

source_name: BYrpd3 20 min after shift to 37C in YPD


title: HS2_wt_10 min

source_name: BY4741 10 min after shift to 37C in YPD


title: HS2_rpd3_10 min

source_name: BYrpd3 10 min after shift to 37C in YPD


title: HS1_rpd3_15 min

source_name: BYrpd3 15 min after shift to 37C in YPD


title: HS1_rpd3_60 min

source_name: BYrpd3 60 min after shift to 37C in YPD


title: HS2_wt_30 min

source_name: BY4741 30 min after shift to 37C in YPD


title: HS2_rpd3_30 min

source_name: BYrpd3 30 min after shift to 37C in YPD


title: HS2_rpd3_5 min


title: HS2_wt_20 min

source_name: BY4741 20 min after shift to 37C in YPD


title: HS2_rpd3_60 min


title: NaCl2_wt_30 min

description: Comparison of wt before and after addition of NaCl to 0.7M in YPD - replicate #2

source_name: BY4741 30 min after addition of NaCl to 0.75M

source_name: BY4741 grown in YPD at 30C (time 0 reference)


title: HS1_rpd3_30 min


title: HS1_wt_60 min

description: Comparison of wt before and after heat shock from 25C to 37C - replicate #1


title: HS1_wt_5 min


title: HS1_wt_30 min


title: rpd3 vs WT_3

description: Comparison of WT and rpd3 basal expression replicate #3

source_name: BY4741 grown in YPD  replicate #3

source_name: BYrpd3 grown in YPD replicate #3


title: HS1_wt_15 min

source_name: BY4741 grown in YPD at 25C (time 0 reference)

source_name: BY4741 15 min after shift to 37C in YPD


title: rpd3 vs WT_2

description: Comparison of  rpd3 and WT basal expression replicate #2

source_name: BYrpd3 grown in YPD replicate #2

source_name: BY4741 grown in YPD  replicate #2


title: rpd3 vs WT_1

description: Comparison of  rpd3 and WT basal expression replicate #1

source_name: BYrpd3 grown in YPD replicate #1

source_name: BY4741 grown in YPD  replicate #1


title: HuR_LCKCRE_0hr_2

status: Public on May 20 2009

city: Durham

first: Neelanjan

last: Mukherjee

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences & Policy

institute: Duke University

description:
Total thymocytes were isolated from female 6-8 week old LckCre+ Elavl1+, LckCre+Elavl1fl/fl
and Elavlfl/fl thymi following desegregation and pooled from n=6 littermate mice/group,
were cultured in complete RPMI-1640 medium the presence or absence of PMA (10 ng/ml) and
ionomycin (500ng/ml). Cells were collected at 0, 4 and 12 hrs post stimulation and washed
in ice cold PBS via centrifugation, prior to lysis with Trizol (Invitrogen). Total RNA was
then treated with DNase I to minimize contamination from genomic DNA. Further purification
was carried out using the RNeasy columns (Qiagen). The experiment was performed two more times
to complete a set of 3 biological replicates.
Arrays were printed at the Duke Microarray Facility using the Genomics Solutions
OmniGrid 300 Arrayer. The arrays contain the mouse Operon v3.0 arrays (Oligo
Source) that possess 34,602 unique optimized 70-mers.
RNA quality was ascertained using an Agilent 2100 bioanalyzer (Agilent technologies).
Total RNA (10 µg) from each sample and the reference (Universal mouse Reference
RNA, Stratagene) were hybridized to oligo (dT) primers at 65º C and then incubated at
42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or
Cy3-dCTP, and a deoxynucleotide mix. In all cases, Ex vivo RNA samples were
labeled with Cy3 and reference samples were labeled with Cy5. NaOH was used to
destroy residual RNA. Sample and reference cDNA were then pooled, purified with
QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50%
formamide, 5 SSC, and 0.1% SDS), COT-1 DNA, and poly-deoxyadenylic acid to limit
nonspecific binding, and heated to 95º C for 2 minutes. This mixture was pipetted onto a
microarray slide, and hybridized overnight at 42º C on the MAUI hybridization system
(BioMicro Systems). The array was then washed at increasing stringencies and scanned
on a GenePix 4000B microarray scanner (Axon Instruments). All protocols are available
in greater detail on the Duke Microarray Facility Web site
Lowess normalization was performed within and between all 27 arrays (biological triplicates,
3 strains at 3 time points) using GENESPRING.  During preprocessing a probe was removed from
further consideration in all 27 arrays if it had a "no data" call in even 1 of the 27 arrays.
13,150 probes out of the initial 31,833 probes passed these requirements.

organism: Mus musculus

source_name: HuR LCKCRE ex vivo activation 0hr

extract_protocol: Total RNA was treated with DNase I to minimize contamination from genomic DNA. Further purification was carried out using the RNeasy columns (Qiagen).

tag: Total thymocytes were isolated from female 6-8 week old LckCre+ Elavl1+ thymi following desegregation and pooled from n=6 littermate mice/group, were cultured in complete RPMI-1640 medium the presence or absence of PMA (10 ng/ml) and ionomycin (500ng/ml). Cells were collected at 0, 4 and 12 hrs post stimulation.


title: HuR_ff_12hr_3

hyb_protocol: RNA quality was ascertained using an Agilent 2100 bioanalyzer (Agilent technologies). Total RNA (10 µg) from each sample and the reference (Universal mouse Reference RNA, Stratagene) were hybridized to oligo (dT) primers at 65º C and then incubated at 42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or Cy3-dCTP, and a deoxynucleotide mix. In all cases, Ex vivo RNA samples were labeled with Cy3 and reference samples were labeled with Cy5. NaOH was used to destroy residual RNA. Sample and reference cDNA were then pooled, purified with QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50% formamide, 5 SSC, and 0.1% SDS), COT-1 DNA, and poly-deoxyadenylic acid to limit nonspecific binding, and heated to 95º C for 2 minutes. This mixture was pipetted onto a microarray slide, and hybridized overnight at 42º C on the MAUI hybridization system (BioMicro Systems). The array was then washed at increasing stringencies and scanned on a GenePix 4000B microarray scanner (Axon Instruments). All protocols are available in greater detail on the Duke Microarray Facility Web site

data_processing:
Lowess normalization was performed within and between all 27 arrays (biological triplicates,
3 strains at 3 time points) using GENESPRING.  During preprocessing a probe was removed from
further consideration in all 27 arrays if it had a "no data" call in even 1 of the 27 arrays.
13,150 probes out of the initial 31,833 probes passed these requirements.

source_name: HuR floxed ex vivo activation 12hr

tag: Total thymocytes were isolated from female 6-8 week old Elavlfl/fl thymi following desegregation and pooled from n=6 littermate mice/group, were cultured in complete RPMI-1640 medium the presence or absence of PMA (10 ng/ml) and ionomycin (500ng/ml). Cells were collected at 0, 4 and 12 hrs post stimulation.


title: HuR_KO_12hr_1

scan_protocol: RNA quality was ascertained using an Agilent 2100 bioanalyzer (Agilent technologies). Total RNA (10 µg) from each sample and the reference (Universal mouse Reference RNA, Stratagene) were hybridized to oligo (dT) primers at 65º C and then incubated at 42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or Cy3-dCTP, and a deoxynucleotide mix. In all cases, Ex vivo RNA samples were labeled with Cy3 and reference samples were labeled with Cy5. NaOH was used to destroy residual RNA. Sample and reference cDNA were then pooled, purified with QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50% formamide, 5 SSC, and 0.1% SDS), COT-1 DNA, and poly-deoxyadenylic acid to limit nonspecific binding, and heated to 95º C for 2 minutes. This mixture was pipetted onto a microarray slide, and hybridized overnight at 42º C on the MAUI hybridization system (BioMicro Systems). The array was then washed at increasing stringencies and scanned on a GenePix 4000B microarray scanner (Axon Instruments). All protocols are available in greater detail on the Duke Microarray Facility Web site

source_name: HuR KO ex vivo activation 12hr

tag: Total thymocytes were isolated from female 6-8 week old LckCre+Elavl1fl/fl thymi following desegregation and pooled from n=6 littermate mice/group, were cultured in complete RPMI-1640 medium the presence or absence of PMA (10 ng/ml) and ionomycin (500ng/ml). Cells were collected at 0, 4 and 12 hrs post stimulation.


title: HuR_LCKCRE_12hr_2

source_name: HuR LCKCRE ex vivo activation 12hr

label_protocol:
RNA quality was ascertained using an Agilent 2100 bioanalyzer (Agilent technologies).
Total RNA (10 µg) from each sample and the reference (Universal mouse Reference
RNA, Stratagene) were hybridized to oligo (dT) primers at 65º C and then incubated at
42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or
Cy3-dCTP, and a deoxynucleotide mix. In all cases, Ex vivo RNA samples were
labeled with Cy3 and reference samples were labeled with Cy5. NaOH was used to
destroy residual RNA. Sample and reference cDNA were then pooled, purified with
QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50%
formamide, 5 SSC, and 0.1% SDS), COT-1 DNA, and poly-deoxyadenylic acid to limit
nonspecific binding, and heated to 95º C for 2 minutes. This mixture was pipetted onto a
microarray slide, and hybridized overnight at 42º C on the MAUI hybridization system
(BioMicro Systems). The array was then washed at increasing stringencies and scanned
on a GenePix 4000B microarray scanner (Axon Instruments). All protocols are available
in greater detail on the Duke Microarray Facility Web site


title: HuR_ff_12hr_1

source_name: Universal mouse Reference RNA, Stratagene


title: HuR_ff_12hr_2

tag: Universal mouse Reference RNA, Stratagene


title: HuR_LCKCRE_0hr_3


title: HuR_LCKCRE_12hr_3


title: HuR_ff_4hr_2

source_name: HuR floxed ex vivo activation 4hr


title: HuR_ff_4hr_3


title: HuR_ff_0hr_3

source_name: HuR floxed ex vivo activation 0hr


title: HuR_LCKCRE_4hr_1

source_name: HuR LCKCRE ex vivo activation 4hr


title: HuR_KO_12hr_3


title: HuR_ff_4hr_1


title: HuR_KO_4hr_1

source_name: HuR KO ex vivo activation 4hr


title: HuR_ff_0hr_2


title: HuR_LCKCRE_12hr_1


title: HuR_LCKCRE_0hr_1


title: HuR_LCKCRE_4hr_2


title: HuR_KO_12hr_2


title: HuR_ff_0hr_1


title: HuR_KO_0hr_3

source_name: HuR KO ex vivo activation 0hr


title: HuR_KO_4hr_3


title: HuR_KO_4hr_2


title: HuR_KO_0hr_2


title: HuR_KO_0hr_1


title: HuR_LCKCRE_4hr_3


title: Kidney BXD38 vs C57BL/6J

status: Public on May 19 2009

city: University of New South Wales

first: Mark

last: Cowley

state: NSW

address: School of BABS, Building D26

department: Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

hyb_protocol: Labeled cDNA was directly compared on a single glass slide two-color microarray containing the Compugen Mouse OligoLibrary representing 21,997 genes and Lucidea Universal ScoreCard (Clive and Vera Ramaciotti Center for Gene Function Analysis, UNSW, Sydney, Australia), in 100 ul of DIGEasy buffer (Roche, Basel, Switzerland) with 5 uL each yeast tRNA and calf thymus DNA as blockers (Invitrogen, Mt. Waverley, Vic, Australia). Utility controls from the Lucidea Scorecard were not used, and therefore served as additional negative controls. Hybridized microarrays were washed in 1xSSC, three times in 1xSSC, 0.1%SDS at 50 deg. C, and three times in 1xSSC, dried by centrifugation.

scan_protocol: GenePix 4000B microarray scanner (Axon Instruments, Union City, CA, USA).

data_processing: Image analysis was performed with the Spot image analysis software version 2 (CSIRO, Australia). All further data processing and statistical analyses were performed using R version 2.0.0 (17). Gene expression data were morph background corrected and log2 transformed. Data for controls and the 232 replicated spots of the housekeeping gene Gapd (NM_008084) were removed prior to normalization to avoid bias. All 31 slides were normalized using print-tip loess (R/limma package) and then applied quantile normalization across arrays.

label: Alexa Fluor 647

source_name: Total RNA from whole brain, BxD/TyJ strain 38

label_protocol: Equal amounts of total RNA from three replicates of each strain were mixed to give a tissue pool representative of the genetic background. 20 ug of pooled RNA was reverse transcribed (SuperScript III Indirect cDNA Labeling System, Invitrogen, Mt. Waverley, Vic, Australia) and fluorescently labeled with Alexa Fluor 647.

extract_protocol: Total RNA was extracted according to the manufacturer's instructions with Trizol Reagent (Invitrogen, Mt.Waverley, Vic, Australia); purity and integrity was assessed by OD_260/OD_280 readings greater than 2 and intact rRNA bands analysis (Agilent Bioanalyzer, Agilent, Forest Hills, Vic, Australia), respectively.

tag: strain

value: BXD/TyJ strain 38

tag: Gender

value: male

tag: Age

value: Eight weeks

tag: Tissue

value: Whole Brain

label: Alexa Fluor 555

source_name: whole brain, C57BL/6J

label_protocol: 20 ug of pooled RNA and 2 ug of Lucidea Universal Scorecard Spike-in (Amersham Biosciences, Castle Hill, NSW, Australia) were reverse transcribed using the SuperScript III Indirect cDNA Labeling System (Invitrogen, Mt. Waverley, Vic, Australia) and fluorescently labeled with Alexa Fluor 555


title: Kidney BXD42 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 42

value: BXD/TyJ strain 42

tag: Strain


title: Kidney BXD40 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 40

value: BXD/TyJ strain 40


title: Kidney BXD24 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 24

value: BXD/TyJ strain 24


title: Kidney BXD23 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 23

value: BXD/TyJ strain 23


title: Kidney BXD19 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 19

value: BXD/TyJ strain 19


title: Kidney BXD36 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 36

value: BXD/TyJ strain 36


title: Kidney BXD28 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 28

value: BXD/TyJ strain 28


title: Kidney BXD27 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 27

value: BXD/TyJ strain 27


title: Kidney BXD20 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 20

value: BXD/TyJ strain 20


title: Kidney BXD15 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 15

value: BXD/TyJ strain 15


title: Kidney BXD32 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 32

value: BXD/TyJ strain 32


title: Kidney BXD22 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 22

value: BXD/TyJ strain 22


title: Kidney BXD12 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 12

value: BXD/TyJ strain 12


title: Kidney BXD29 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 29

value: BXD/TyJ strain 29


title: Kidney BXD39 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 39

value: BXD/TyJ strain 39

value: male


title: Kidney BXD13 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 13

value: BXD/TyJ strain 13

value: Eight weeks

value: Whole Brain


title: Kidney BXD14 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 14

value: BXD/TyJ strain 14

source_name: whole brain, C57BL/6J


title: Kidney BXD9 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 9

value: BXD/TyJ strain 9


title: Kidney BXD31 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 31

value: BXD/TyJ strain 31


title: Kidney BXD33 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 33

value: BXD/TyJ strain 33


title: Kidney BXD34 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 34

value: BXD/TyJ strain 34


title: Kidney BXD18 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 18

value: BXD/TyJ strain 18


title: Kidney BXD6 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 6

value: BXD/TyJ strain 6


title: Kidney BXD16 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 16

value: BXD/TyJ strain 16


title: Kidney BXD8 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 8

value: BXD/TyJ strain 8


title: Kidney BXD11 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 11

value: BXD/TyJ strain 11


title: Kidney BXD21 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 21

value: BXD/TyJ strain 21


title: Kidney BXD2 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 2

value: BXD/TyJ strain 2


title: Kidney BXD5 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 5

value: BXD/TyJ strain 5


title: Brain BXD38 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 38

value: BXD/TyJ strain 38

value: male


title: Kidney BXD1 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 1

value: BXD/TyJ strain 1

value: Eight weeks


title: Brain BXD33 vs C57BL/6J

value: Whole Brain


title: Brain BXD42 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 42

value: BXD/TyJ strain 42


title: Brain BXD29 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 29

value: BXD/TyJ strain 29


title: Brain BXD36 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 36

value: BXD/TyJ strain 36

source_name: whole brain, C57BL/6J


title: Brain BXD28 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 28

value: BXD/TyJ strain 28


title: Brain BXD23 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 23

value: BXD/TyJ strain 23


title: Brain BXD21 vs C57BL/6J


title: Brain BXD32 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 32

value: BXD/TyJ strain 32


title: Brain BXD39 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 39

value: BXD/TyJ strain 39


title: Brain BXD15 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 15

value: BXD/TyJ strain 15


title: Brain BXD22 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 22

value: BXD/TyJ strain 22


title: Brain BXD16 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 16

value: BXD/TyJ strain 16


title: Brain BXD27 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 27

value: BXD/TyJ strain 27


title: Brain BXD31 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 31

value: BXD/TyJ strain 31


title: Brain BXD20 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 20

value: BXD/TyJ strain 20


title: Brain BXD18 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 18

value: BXD/TyJ strain 18

value: male


title: Brain BXD13 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 13

value: BXD/TyJ strain 13

value: Eight weeks


title: Brain BXD40 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 40

value: BXD/TyJ strain 40

value: Whole Brain


title: Brain BXD34 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 34

value: BXD/TyJ strain 34


title: Brain BXD11 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 11

value: BXD/TyJ strain 11


title: Brain BXD14 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 14

value: BXD/TyJ strain 14


title: Brain BXD6 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 6

value: BXD/TyJ strain 6

source_name: whole brain, C57BL/6J


title: Brain BXD9 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 9

value: BXD/TyJ strain 9


title: Brain BXD8 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 8

value: BXD/TyJ strain 8


title: Brain BXD24 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 24

value: BXD/TyJ strain 24


title: Brain BXD12 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 12

value: BXD/TyJ strain 12


title: Brain BXD19 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 19

value: BXD/TyJ strain 19


title: Brain BXD2 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 2

value: BXD/TyJ strain 2


title: Brain BXD5 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 5

value: BXD/TyJ strain 5


title: Brain BXD1 vs C57BL/6J

source_name: Total RNA from whole brain, BxD/TyJ strain 1

value: BXD/TyJ strain 1


title: PBMC Exposed, biological rep 6 (HG-U133B)

status: Public on May 11 2009

city: Berkeley

first: Cliona

last: McHale

state: CA

address: 384 Li Ka Shing Center

department: School of Public Health

institute: University of California Berkeley

description: biotin

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133A and B chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner GA 2500.

data_processing: RMA (robust multi-chip averaging) from the Bioconductor Affymetrix package was used for quantile normalization and background adjustment.

label: biotin

organism: Homo sapiens

source_name: PBMC Exposed

label_protocol: Biotinylated cRNAs were prepared according to the GeneChip Eukaryotic Small Sample Target Labeling Assay Version II (Affymetrix 2003a), with the exception that the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) was used instead of ethanol precipitation. Total RNA (100 ng) was amplified for each sample, with 400 ng of first-round cRNA used for the second round of cDNA synthesis.

extract_protocol: Peripheral blood was collected from each subject at the beginning of the workday around 0900 hr and processed within 6 hr of collection. PBMC were isolated by Ficoll-Paque and lysed in RLT buffer (Qiagen). Lysates were frozen at -80°C and later thawed and extracted using Qiagen's RNeasy mini kit according to the manufacturer's instructions.

tag: Male


title: PBMC Exposed, biological rep 3 (HG-U133B)

description: biotin


title: PBMC Exposed, biological rep 7 (HG-U133A)

description: biotin

tag: Female


title: PBMC Exposed, biological rep 1 (HG-U133A)

description: biotin


title: PBMC Exposed, biological rep 8 (HG-U133A)

description: biotin


title: PBMC Exposed, biological rep 2 (HG-U133A)

description: biotin


title: PBMC Control, biological rep 3 (HG-U133A)

description: biotin

source_name: PBMC Control


title: PBMC Control, biological rep 4 (HG-U133A)

description: biotin


title: PBMC Control, biological rep 8 (HG-U133B)

description: biotin


title: PBMC Exposed, biological rep 7 (HG-U133B)

description: biotin


title: PBMC Exposed, biological rep 8 (HG-U133B)

description: biotin


title: PBMC Control, biological rep 6 (HG-U133A)

description: biotin


title: PBMC Exposed, biological rep 5 (HG-U133B)

description: biotin


title: PBMC Exposed, biological rep 4 (HG-U133A)

description: biotin


title: PBMC Exposed, biological rep 3 (HG-U133A)

description: biotin


title: PBMC Control, biological rep 7 (HG-U133B)

description: biotin


title: PBMC Exposed, biological rep 2 (HG-U133B)

description: biotin


title: PBMC Exposed, biological rep 6 (HG-U133A)

description: biotin


title: PBMC Control, biological rep 8 (HG-U133A)

description: biotin


title: PBMC Control, biological rep 2 (HG-U133A)

description: biotin


title: PBMC Control, biological rep 5 (HG-U133A)

description: biotin


title: PBMC Exposed, biological rep 5 (HG-U133A)

description: biotin


title: PBMC Control, biological rep 6 (HG-U133B)

description: biotin


title: PBMC Control, biological rep 7 (HG-U133A)

description: biotin


title: PBMC Exposed, biological rep 1 (HG-U133B)

description: biotin


title: PBMC Control, biological rep 3 (HG-U133B)

description: biotin


title: PBMC Control, biological rep 4 (HG-U133B)

description: biotin


title: PBMC Exposed, biological rep 4 (HG-U133B)

description: biotin


title: PBMC Control, biological rep 5 (HG-U133B)

description: biotin


title: PBMC Control, biological rep 1 (HG-U133A)

description: biotin


title: PBMC Control, biological rep 1 (HG-U133B)

description: biotin


title: PBMC Control, biological rep 2 (HG-U133B)

description: biotin


title: Cyanidioschyzon merolae cell cycle3_10h

status: Public on May 08 2009

city: Toshima-ku

first: Takayuki

last: Fujiwara

department: Life Science

institute: Rikkyo University

description: C. merolae cells at a certain timepoint to look at mitotic and organelle cell division

hyb_protocol: Hybridization solution (5x SSC, 0.5%SDS, 4xDenhalt’s solution, 10% formamid, 100ng/μl Salmon Sperm DNA) and Cy3-congugated aRNA was hybridized to spotted microarray slides covered with a coverglass (Matsunami) in a slide hybridization chamber (Sigma) for 18 hours at 55°C. Hybridized slides were washed in 1× SSC/0.03% SDS for 6 min at 45°C, followed by 0.2× SSC for 5 min, and 0.05× SSC for 4 min, and then spin-dried before scanning.

scan_protocol: Microarray slides were scanned using a FLA-8000 scanner (FujiFilm) at a wavelength of 532nm and 635nm with 5μm resolution. Gene Spot signals on microarray images were measured by the microarray analyzing software ArrayGauge Ver.2 (FujiFilm).

data_processing: Global normalization was performed by Ver.2 ArrayGauge (FujiFilm) as total of the gene spot signals becomes equal in each channels. Then ratio of normalized cy3 and cy5 signals were made a logarithm.

organism: Cyanidioschyzon merolae

source_name: Cyanidioschyzon merolae cell cycle3_10h

label_protocol: Amino-allyl aRNA was synthesized using an Amino-Allyl MessageAmp aRNA Kit (Ambion, Texas, USA) according to the manufacturer's instructions. It was transcribed in the presence of amino-allyl dUTP by templating double strand cDNA synthesized using T7 oligo(dT) primer. Cy3-congugated aRNA was prepared by mixing cy3 (GE Healthcare 1vial/45ul dissolved in DMSO) and 5μg amino-allyl aRNA in cuppling buffer (0.1M NaHCO3 pH9.0), incubating for 60min at 40°C and then purified by a Bio Spin-Column (Bio-Rad) and microcon-YM30 spin-column (Millipore).

extract_protocol: Nucleus isolation buffer (50mM Tris-HCl pH7.6、100mM EDTA、300mM NaCl、4% SDS、2%N-Lauroylsarcosine Sodium Salt) pre-warmed at 60°C was added to the frozen cell pellets. The lysate was added to an equal volume of PCI (phenol: Chloroform: Isoamylalcohol = 25: 24: 1). The aqueous phase was recovered by centrifuging at 15,000 x g for 5 min at 4°C and re-extracted using PCI. Total nucleus acid was precipitated by adding an equal volume of isopropanol and recovered by centrifugation at 15,000 x g for 15 min at 4°C. The pellet was melted in DNase I solution ( 0.1unit/μl DNase I, RNase Free ; Roshe、0.4unit/μl RNase Inhibitor ; Sigma、10mM DTT、10mM MgCl) and incubated for 45min at 37°C. Total RNA was precipitated by adding an equal volume of isopropanol and recovered by centrifugation at 15,000 x g for 15 min at 4°C.

value: Cyanidioschyzon merolae 10D

source_name: The mixture of each sample in C.merolae cell cycle

label_protocol: Amino-allyl aRNA was synthesized using an Amino-Allyl MessageAmp aRNA Kit (Ambion, Texas, USA) according to the manufacturer's instructions. It was transcribed in the presence of amino-allyl dUTP by templating double strand cDNA synthesized using T7 oligo(dT) primer. Cy5-congugated aRNA was prepared by mixing cy5 (GE Healthcare 1vial/45ul dissolved in DMSO) and 5μg amino-allyl aRNA in cuppling buffer (0.1M NaHCO3 pH9.0), incubating for 60min at 40°C and then purified by a Bio Spin-Column (Bio-Rad) and microcon-YM30 spin-column (Millipore).


title: Cyanidioschyzon merolae cell cycle3_28h

source_name: Cyanidioschyzon merolae cell cycle3_28h


title: Cyanidioschyzon merolae cell cycle3_26h

source_name: Cyanidioschyzon merolae cell cycle3_26h


title: Cyanidioschyzon merolae cell cycle3_30h

source_name: Cyanidioschyzon merolae cell cycle3_30h


title: Cyanidioschyzon merolae cell cycle3_18h

source_name: Cyanidioschyzon merolae cell cycle3_18h


title: Cyanidioschyzon merolae cell cycle3_34h

source_name: Cyanidioschyzon merolae cell cycle3_34h


title: Cyanidioschyzon merolae cell cycle3_16h

source_name: Cyanidioschyzon merolae cell cycle3_16h


title: Cyanidioschyzon merolae cell cycle3_4h

source_name: Cyanidioschyzon merolae cell cycle3_4h


title: Cyanidioschyzon merolae cell cycle3_12h

source_name: Cyanidioschyzon merolae cell cycle3_12h


title: Cyanidioschyzon merolae cell cycle3_48h

source_name: Cyanidioschyzon merolae cell cycle3_48h


title: Cyanidioschyzon merolae cell cycle3_32h

source_name: Cyanidioschyzon merolae cell cycle3_32h


title: Cyanidioschyzon merolae cell cycle3_50h

source_name: Cyanidioschyzon merolae cell cycle3_50h


title: Cyanidioschyzon merolae cell cycle3_40h

source_name: Cyanidioschyzon merolae cell cycle3_40h


title: Cyanidioschyzon merolae cell cycle3_8h

source_name: Cyanidioschyzon merolae cell cycle3_8h


title: Cyanidioschyzon merolae cell cycle3_24h

source_name: Cyanidioschyzon merolae cell cycle3_24h


title: Cyanidioschyzon merolae cell cycle3_20h

source_name: Cyanidioschyzon merolae cell cycle3_20h


title: Cyanidioschyzon merolae cell cycle3_22h

source_name: Cyanidioschyzon merolae cell cycle3_22h


title: Cyanidioschyzon merolae cell cycle3_44h

source_name: Cyanidioschyzon merolae cell cycle3_44h

source_name: The mixture of each sample in C.merolae cell cycle


title: Cyanidioschyzon merolae cell cycle3_42h

source_name: Cyanidioschyzon merolae cell cycle3_42h


title: Cyanidioschyzon merolae cell cycle3_46h

source_name: Cyanidioschyzon merolae cell cycle3_46h


title: Cyanidioschyzon merolae cell cycle3_38h

source_name: Cyanidioschyzon merolae cell cycle3_38h


title: Cyanidioschyzon merolae cell cycle3_6h

source_name: Cyanidioschyzon merolae cell cycle3_6h


title: Cyanidioschyzon merolae cell cycle3_36h

source_name: Cyanidioschyzon merolae cell cycle3_36h


title: Cyanidioschyzon merolae cell cycle3_14h

source_name: Cyanidioschyzon merolae cell cycle3_14h


title: Cyanidioschyzon merolae cell cycle3_2h

source_name: Cyanidioschyzon merolae cell cycle3_2h


title: Cyanidioschyzon merolae cell cycle2_50h

source_name: Cyanidioschyzon merolae cell cycle2_50h


title: Cyanidioschyzon merolae cell cycle2_48h

source_name: Cyanidioschyzon merolae cell cycle2_48h


title: Cyanidioschyzon merolae cell cycle2_46h

source_name: Cyanidioschyzon merolae cell cycle2_46h


title: Cyanidioschyzon merolae cell cycle2_44h

source_name: Cyanidioschyzon merolae cell cycle2_44h


title: Cyanidioschyzon merolae cell cycle2_42h

source_name: Cyanidioschyzon merolae cell cycle2_42h


title: Cyanidioschyzon merolae cell cycle2_10h

source_name: Cyanidioschyzon merolae cell cycle2_10h


title: Cyanidioschyzon merolae cell cycle2_34h

source_name: Cyanidioschyzon merolae cell cycle2_34h


title: Cyanidioschyzon merolae cell cycle2_32h

source_name: Cyanidioschyzon merolae cell cycle2_32h


title: Cyanidioschyzon merolae cell cycle2_40h

source_name: Cyanidioschyzon merolae cell cycle2_40h


title: Cyanidioschyzon merolae cell cycle2_8h

source_name: Cyanidioschyzon merolae cell cycle2_8h

source_name: The mixture of each sample in C.merolae cell cycle


title: Cyanidioschyzon merolae cell cycle2_26h

source_name: Cyanidioschyzon merolae cell cycle2_26h


title: Cyanidioschyzon merolae cell cycle2_6h

source_name: Cyanidioschyzon merolae cell cycle2_6h


title: Cyanidioschyzon merolae cell cycle2_38h

source_name: Cyanidioschyzon merolae cell cycle2_38h


title: Cyanidioschyzon merolae cell cycle2_28h

source_name: Cyanidioschyzon merolae cell cycle2_28h


title: Cyanidioschyzon merolae cell cycle2_4h

source_name: Cyanidioschyzon merolae cell cycle2_4h


title: Cyanidioschyzon merolae cell cycle2_14h

source_name: Cyanidioschyzon merolae cell cycle2_14h


title: Cyanidioschyzon merolae cell cycle2_30h

source_name: Cyanidioschyzon merolae cell cycle2_30h


title: Cyanidioschyzon merolae cell cycle2_2h

source_name: Cyanidioschyzon merolae cell cycle2_2h


title: Cyanidioschyzon merolae cell cycle2_16h

source_name: Cyanidioschyzon merolae cell cycle2_16h


title: Cyanidioschyzon merolae cell cycle2_18h

source_name: Cyanidioschyzon merolae cell cycle2_18h


title: Cyanidioschyzon merolae cell cycle1_36h

hyb_protocol: Hybridization solution (5x SSC, 0.5%SDS, 4xDenhalt’s solution, 10% formamid, 100ng/μl Salmon Sperm DNA) and Cy-congugated aRNA was hybridized to spotted microarray slides covered with a coverglass (Matsunami) in a slide hybridization chamber (Sigma) for 18 hours at 55°C. Hybridized slides were washed in 1× SSC/0.03% SDS for 6 min at 45°C, followed by 0.2× SSC for 5 min, and 0.05× SSC for 4 min, and then spin-dried before scanning.

source_name: Cyanidioschyzon merolae cell cycle1_36h


title: Cyanidioschyzon merolae cell cycle2_20h

source_name: Cyanidioschyzon merolae cell cycle2_20h


title: Cyanidioschyzon merolae cell cycle2_24h

source_name: Cyanidioschyzon merolae cell cycle2_24h


title: Cyanidioschyzon merolae cell cycle1_50h

source_name: Cyanidioschyzon merolae cell cycle1_50h


title: Cyanidioschyzon merolae cell cycle2_22h

source_name: Cyanidioschyzon merolae cell cycle2_22h


title: Cyanidioschyzon merolae cell cycle1_42h

source_name: Cyanidioschyzon merolae cell cycle1_42h


title: Cyanidioschyzon merolae cell cycle1_48h

source_name: Cyanidioschyzon merolae cell cycle1_48h

source_name: The mixture of each sample in C.merolae cell cycle


title: Cyanidioschyzon merolae cell cycle1_38h

source_name: Cyanidioschyzon merolae cell cycle1_38h


title: Cyanidioschyzon merolae cell cycle2_36h

source_name: Cyanidioschyzon merolae cell cycle2_36h

treatment_protocol: Strain: Cyanidioschyzon merolae 10D


title: Cyanidioschyzon merolae cell cycle1_40h

source_name: Cyanidioschyzon merolae cell cycle1_40h

tag: Cyanidioschyzon merolae cell cycle1_40h


title: Cyanidioschyzon merolae cell cycle1_44h

source_name: Cyanidioschyzon merolae cell cycle1_44h


title: Cyanidioschyzon merolae cell cycle1_46h

source_name: Cyanidioschyzon merolae cell cycle1_46h


title: Cyanidioschyzon merolae cell cycle2_12h

source_name: Cyanidioschyzon merolae cell cycle2_12h


title: Cyanidioschyzon merolae cell cycle1_32h

source_name: Cyanidioschyzon merolae cell cycle1_32h


title: Cyanidioschyzon merolae cell cycle1_34h

source_name: Cyanidioschyzon merolae cell cycle1_34h


title: Cyanidioschyzon merolae cell cycle1_28h

source_name: Cyanidioschyzon merolae cell cycle1_28h


title: Cyanidioschyzon merolae cell cycle1_30h

source_name: Cyanidioschyzon merolae cell cycle1_30h


title: Cyanidioschyzon merolae cell cycle1_24h

source_name: Cyanidioschyzon merolae cell cycle1_24h


title: Cyanidioschyzon merolae cell cycle1_20h

source_name: Cyanidioschyzon merolae cell cycle1_20h


title: Cyanidioschyzon merolae cell cycle1_8h

source_name: Cyanidioschyzon merolae cell cycle1_8h


title: Cyanidioschyzon merolae cell cycle1_14h

source_name: Cyanidioschyzon merolae cell cycle1_14h


title: Cyanidioschyzon merolae cell cycle1_10h

source_name: Cyanidioschyzon merolae cell cycle1_10h


title: Cyanidioschyzon merolae cell cycle1_22h

source_name: Cyanidioschyzon merolae cell cycle1_22h


title: Cyanidioschyzon merolae cell cycle1_18h

source_name: Cyanidioschyzon merolae cell cycle1_18h

source_name: The mixture of each sample in C.merolae cell cycle


title: Cyanidioschyzon merolae cell cycle1_26h

source_name: Cyanidioschyzon merolae cell cycle1_26h


title: Cyanidioschyzon merolae cell cycle1_12h

source_name: Cyanidioschyzon merolae cell cycle1_12h


title: Cyanidioschyzon merolae cell cycle1_4h

source_name: Cyanidioschyzon merolae cell cycle1_4h


title: Cyanidioschyzon merolae cell cycle1_6h

source_name: Cyanidioschyzon merolae cell cycle1_6h


title: Cyanidioschyzon merolae cell cycle1_16h

source_name: Cyanidioschyzon merolae cell cycle1_16h


title: Cyanidioschyzon merolae cell cycle1_2h

source_name: Cyanidioschyzon merolae cell cycle1_2h


title: Primary Langerhans cells with TCDD

status: Public on May 01 2009

city: Dusseldorf

first: Charlotte

last: Esser

address: Auf´m Hennekamp 50

department: Molecular Immunology

country: Germany

institute: IUF

description: Langerhans cells treated in vivo with 10ug TCDD after 24 hours

hyb_protocol: Standard Affymetric protocol

scan_protocol: Standard Affymetric protocol

data_processing: The resulting CEL files were analyzed with the bioconductor affy package using the MAS5.0 algorithm.

source_name: Primary Langerhans cells from mice treated with TCDD

label_protocol: MessageAmp™ Kit of Ambion (Woodward St. Austin, USA) for amplificaton. RNA was biotinylated (Enzo Bio Array™HighYield™ RNA transcript labeling kit (Affymetrix, High Wycombe, UK)) and purified.

extract_protocol: Trizol

treatment_protocol: 100µl TCDD in oil in vivo treatment, isolation after 24 hours

tag: C57BL/6, female mice, 6-10 weeks old; SPF husbandry


title: Primary Langerhans cells from back skin

description: Primary Langerhans cells from back skin; 24 hours control experiment Nov2004

source_name: Primary Langerhans cells from back skin

treatment_protocol: 100µl TCDD, i.p. in  DMSO/oil in vivo treatment, isolation of cells after 24 hours

tag: C57BL/6, female mice, 6-10 weeks old, SPF husbandry


title: Primary Langerhans cells

description: Langerhans cells; 24 hours control experiment Jan2005

source_name: Primary Langerhans cells

treatment_protocol: 100µl DMSO/olive oil in vivo, treatment in vivo, isolation after 24 hours

tag: sorted from back skin epidermis to more than 95% purity


title: NR-S1, primary tumor gamma 8 Gy (Cy5) vs. primary tumor control (Cy3), replicate 1

status: Public on Apr 23 2009

city: Chiba

first: Kaori

last: Imadome

address: Anagawa 4-9-1

department: Research Center of Charged Particle Therapy

institute: National institute of radiological sciences

description: Murine squamous cell carcinoma, NR-S1, was transplanted into the hind leg of C3H/HeMsNrs mice. When the diameter of the primary tumors became 7.5mm, one group received no irradiation, and another group received 8 Gy of gamma ray irradiation on the primary tumors. After 1 week, the primary tumors were sampled, and the tumor cells were collected using the laser microdissection technique. The expression profiles of the non-irradiated primary tumor and gamma-ray-irradiated tumor were compared using the two-color method.

hyb_protocol: according to standard Agilent protocol

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Dye biases between two signals, Red and Green, were corrected using Lowess normalization, subtracted background and converted to log10 of processed Red signal/processed Green signal.

source_name: NR-S1, primary tumor gamma ray 8 Gy, 1 week after 7.5 mm, clone 1

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit

extract_protocol: RNeasy Micro Kit (QIAGEN)

treatment_protocol: Tumor cells were collected selectively by laser-microdissection technique, and the RNA was extracted from the tumor cells.

value: C3H/HeMsNrs, Gender:male, Tumor type:NR-S1 (squamous cell carcinoma), Tumor site:primary tumor (hind leg), Time:1 week after the diameter of the primary tumor had reached 7.5 mm, Irradiation:gamma ray 8 Gy on the primary tumor when the diameter is 7.5 mm

source_name: NR-S1, primary tumor control, 1 week after 7.5 mm, clone 1

value: C3H/HeMsNrs, Gender:male, Tumor type:NR-S1 (squamous cell carcinoma), Tumor site:primary tumor (hind leg), Time:1 week after the diameter of the primary tumor had reached 7.5 mm, Irradiation:None


title: NR-S1, primary tumor control (Cy5) vs. primary tumor carbon 5 Gy (Cy3), replicate 1

description: Murine squamous cell carcinoma, NR-S1, was transplanted into the hind leg of C3H/HeMsNrs mice. When the diameter of the primary tumors became 7.5mm, one group received no irradiation, and another group received 5 Gy of carbon ion irradiation on the primary tumors. After 1 week, the primary tumors were sampled, and the tumor cells were collected using the laser microdissection technique. The expression profiles of the non-irradiated primary tumor and carbon-ion-irradiated tumor were compared using the two-color method.

source_name: NR-S1, primary tumor carbon ion 5 Gy, 1 week after 7.5 mm, clone 1

value: C3H/HeMsNrs, Gender:male, Tumor type:NR-S1 (squamous cell carcinoma), Tumor site:primary tumor (hind leg), Time:1 week after the diameter of the primary tumor had reached 7.5 mm, Irradiation:carbon ion 5 Gy on the primary tumor when the diameter is 7.5 mm


title: Primary Langerhans cells from back skin with TCDD

description: Langerhans cells from back treated in vivo with 10ug TCDD after 24 hours

tag: C57BL/6, female mice, 6-10 weeks old; back skin


title: NR-S1, primary tumor control (Cy5) vs. primary tumor gamma 8 Gy (Cy3), replicate 1


title: NR-S1, primary tumor carbon 5 Gy (Cy5) vs. primary tumor gamma 8 Gy (Cy3), replicate 1

description: Murine squamous cell carcinoma, NR-S1, was transplanted into the hind leg of C3H/HeMsNrs mice. When the diameter of the primary tumors became 7.5mm, one group received 5 Gy of carbon ion irradiation, and another group received 8 Gy of gamma ray irradiation on the primary tumors. After 1 week, the primary tumors were sampled, and the tumor cells were collected using the laser microdissection technique. The expression profiles of the carbon-ion irradiated primary tumor and gamma-ray-irradiated tumor were compared using the two-color method.

value: C3H/HeMsNrs,  Gender:male, Tumor type:NR-S1 (squamous cell carcinoma), Tumor site:primary tumor (hind leg), Time:1 week after the diameter of the primary tumor had reached 7.5 mm, Irradiation:gamma ray 8 Gy on the primary tumor when the diameter is 7.5 mm


title: NPC Ts1/WT_Dye-swap_1

status: Public on Apr 30 2009

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

country: France

institute: INSERM U1127-CNRS UMR7225-UPMC

description: Dye-swap experiment of Ts1Cje versus wild-type NPCs from litter 1.

hyb_protocol: RNG-MRC_MM25k_EVRY microarrays (Le brigand et al., NAR, 2006) were first incubated in a humid chamber for 2 hours to rehydrate the spots then placed for 1 hour in a dessicator and blocked for 1 hour at room temperature in 50mM Sodium Borate pH 9, 0.003% ethanolamine. Slides were then washed 5 minutes with water and dried by centrifugation. Hybridizations were performed in 50% formamide, 5X Denhardt’s, 4x SSC and 0.1% SDS solution at 42°C for 16 hours. Microarrays were then washed at room temperature 5 minutes in 2X SSC, 0.1% SDS, 5 minutes in 1X SSC, 5 minutes in 0.2X SSC and 5 minutes in 0.05X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.

scan_protocol: Microarray images were obtained using a ScanArray Gx scanner (Perkin Elmer). Median signal and median local background intensities were extracted from the images using Mapix v2.2.4 software (Innopsys).

data_processing: For each spot, median signal and median local background intensities were extracted from the images using Mapix v2.2.4 software (Innopsys). Spots which were uninterpretable in all experiments were excluded for further analysis. Filtered data were submitted to VARAN (http://www.bionet.espci.fr) for lowess fit normalisation and log2ratio calculation. Differential expression analysis were performed using VARAN, SAM and t-test.

source_name: WT neurospheres

label_protocol: 5µg of each of the 3 RNA samples were pooled. These 15µg of total RNA were labelled by reverse-transcription in the presence of 7.5µM random hexamers (GE Healthcare), 250µM dUTP-Cy5 (GE Healthcare) and 100U Rtases Reverse-iT Blend (Thermo Scientific) overnight at 37°C.

growth_protocol:
The neocortex was dissected and dissociated to a single cell suspension using a syringe and needle of 18 gauge. The cells were then placed in a flask of NPCM and incubated for up to 5 days in vitro (div) at 37°C in the presence of 5% CO2. NPCM consisted of DMEM:F12 containing Glutamax, 1x B27 supplement, 10ng/µl epidermal growth factor, 10ng/µl basic fibroblast growth factor, 20ng/µl leukaemia inhibitory factor, and penicillin/streptomycin.
After this period of time, neurospheres containing NPCs were split by trituration with the aid of warmed Accumax (Sigma) and a small pipette tip. Such passaged neurospheres were plated at half the density of their precursors. NPCs were cultured in this way for at least four passages (~20 div)

extract_protocol: Total RNA was extracted from each WT neural precursor cells and treated with DNAse using Nucleospin RNA L kit (Macherey-Nagel) according to the manusfacturer’s instructions.

tag: Tissue & Age

value: NPCs of neocortex from 3 littermates wild-type mouse embryos at E14

source_name: Ts1Cje neurospheres

extract_protocol: Total RNA was extracted from each Ts1Cje neural precursor cells and treated with DNAse using Nucleospin RNA L kit (Macherey-Nagel) according to the manusfacturer’s instructions.

value: NPCs of neocortex from 3 littermates Ts1Cje mouse embryos at E14


title: NR-S1, primary tumor gamma 8 Gy (Cy5) vs. primary tumor carbon 5 Gy (Cy3), replicate 1


title: NPC Ts1/WT_Dye-swap_3

description: Dye-swap experiment of Ts1Cje versus wild-type NPCs from litter 3.

growth_protocol: The neocortex was dissected and dissociated to a single cell suspension using a syringe and needle of 18 gauge. The cells were then placed in a flask of NPCM and incubated for up to 5 days in vitro (div) at 37°C in the presence of 5% CO2. NPCM consisted of DMEM:F12 containing Glutamax, 1x B27 supplement, 10ng/µl epidermal growth factor, 10ng/µl basic fibroblast growth factor, 20ng/µl leukaemia inhibitory factor, and penicillin/streptomycin.


title: NPC Ts1/WT_Exp1

description: Transcriptome analysis of Ts1Cje versus wild-type NPCs from litter 1.


title: NR-S1, primary tumor carbon 5 Gy (Cy5) vs. primary tumor control (Cy3), replicate 1

value: C3H/HeMsNrs, Gender:male, Tumor type:NR-S1 (squamous cell carcinoma), Tumor site:primary tumor (hind leg), Time:1 week after the diameter of the primary tumor had reached 7.5 mm , Irradiation:carbon ion 5 Gy on the primary tumor when the diameter is 7.5 mm


title: NPC Ts1/WT_Dye-swap_2

description: Dye-swap experiment of Ts1Cje versus wild-type NPCs from litter 2.


title: NR-S1, lung metastasis carbon 5 Gy (Cy5) vs. primary tumor control (Cy3), replicate 1

description: Murine squamous cell carcinoma, NR-S1, was transplanted into the hind leg of C3H/HeMsNrs mice. The primary tumors were sampled at 1 week after the diameter of the tumor became 7.5mm. Metastatic tumors were sampled at 2 weeks after the diameter of the tumor became 7.5mm and 5 Gy of carbon ion irradiation  is applied to the primary tumor. The tumor cells were collected using the laser microdissection technique, and the expression profiles of the non-irradiated primary tumor and the metastatic tumors of the carbon-ion-irradiated primary tumor were compared using the two-color method.

source_name: NR-S1, lung metastasis carbon ion 5 Gy, 2 weeks after 7.5 mm, clone 1

value: C3H/HeMsNrs, Gender:male, Tumor type:NR-S1 (squamous cell carcinoma), Tumor site:metastasic tumor (lung), Time:2 weeks after the diameter of the primary tumor had reached 7.5 mm, Irradiation:carbon ion 5 Gy on the primary tumor when the diameter is 7.5 mm


title: NR-S1, lung metastasis gamma 8 Gy (Cy5) vs. primary tumor control (Cy3), replicate 1

description: Murine squamous cell carcinoma, NR-S1, was transplanted into the hind leg of C3H/HeMsNrs mice. The primary tumors were sampled at 1 week after the diameter of the tumor became 7.5mm. Metastatic tumors were sampled at 2 weeks after the diameter of the tumor became 7.5mm and 8 Gy of gamma ray irradiation  is applied to the primary tumor. The tumor cells were collected using the laser microdissection technique, and the expression profiles of the non-irradiated primary tumor and the metastatic tumors of the gamma-ray-irradiated primary tumor were compared using the two-color method.

source_name: NR-S1, lung metastasis gamma ray 8 Gy, 2 weeks after 7.5 mm, clone 1

value: C3H/HeMsNrs, Gender:male, Tumor type:NR-S1 (squamous cell carcinoma), Tumor site:metastasic tumor (lung), Time:2 weeks after the diameter of the primary tumor had reached 7.5 mm, Irradiation:gamma ray 8 Gy on the primary tumor when the diameter is 7.5 mm


title: NPC Ts1/WT_Exp2

description: Transcriptome analysis of Ts1Cje versus wild-type NPCs from litter 2.


title: NPC Ts1/WT_Exp3

description: Transcriptome analysis of Ts1Cje versus wild-type NPCs from litter 3.

value: NPCs of neocortex from 3 littermates WT mouse embryos at E14


title: NR-S1, primary tumor control (Cy5) vs. lung metastasis carbon 5 Gy (Cy3), replicate 1


title: Mycelia/Rice vs lesion biological rep 3.2

status: Public on Apr 08 2009

city: Manhattan

first: Barbara

last: Valent

state: KS

address: 4024 Throckmorton Plant Sciences

department: Department of Plant Pathology

institute: Kansas State University

description:
This experiment was designed to compare gene expression
by biotrophic invasive hyphae in planta to gene expression
by mycelium in nutrient medium.

hyb_protocol: The labeled samples (1ug each cy3 and cy5 labeled cRNA) were defragmented by the addition of 25X Agilent Defragmentation buffer and incubated for 30 min, 60°C. The sample was adjusted to a final volume of 450 µl with formamide-containing hybridization buffer (Hughes et al., 2001) and then added to the microarray slides. Slides were incubated for 18 hours with continuous rotation at 40°C. After hybridization, slides were washed in 6X SSPE, 0.005% sarcosyl for 1 min, in 0.06X SSPE for 30 sec, in water for 30 sec and then air dried.

scan_protocol: Slides were scanned on an Agilent G2565BA DNA microarray scanner, and the TIFF images extracted using the Agilent Feature Extraction software (version 8.5). The resultant .xml and .jpeg files were imported into Rosetta Resolver

data_processing: Data from individual biological replicates and also the combined data were analyzed. The data was then plotted as an intensity scatter plot (background subtracted/dye normalized cy3channel vs background subtracted/dye normalized cy5 channel). “Signature sequences” (features which were 1.5 fold differentially regulated, P-values <0.01) were identified by Resolver, and exported to Excel.

organism:
Oryza sativa
Pyricularia oryzae

source_name: 20% mycelial RNA mixed with 80% mock-inoculated rice RNA

label_protocol: Total RNA was labeled using a linear amplification kit (Agilent Technologies). Five hundred nanograms were one-round amplified. Normal cRNA yields were 10-15 ug. The cRNA was labeled according to manufacturers specifications. Fluorescent cRNA was purified, quantified using the NanoDrop Spectrophotometer, and 1 µg of probe was hybridized to M. oryzae microarray slides.

growth_protocol: Inoculated sheath tissues were incubated in high humidity at room temperature for 36 hours. The fungal culture was incubated at 24°C under continuous rotation at 120 RPM. Mycelium was collected by filtration after 24 h of incubation, and the blending treatment was repeated for 3 rounds of growth

extract_protocol: Trizol method as specified by the manufacturers.

treatment_protocol: Sheaths inoculated with gelatin solution. An approximately 1 cm square piece of agar containing fungus was excised from the surface of an oatmeal agar plate and blended in 25 ml of 3,3,3 liquid medium (3g/L of glucose, 3g/L of casamino acids, and 3g/L of yeast extract). The blended mycelium was mixed with 225 ml of fresh medium in 500 ml flasks.

tag: Fungal and plant RNAs mixed in a similar proportion as in the infected samples

source_name: 36 hpi infected rice sheath

growth_protocol: Inoculated tissues were kept in high humidity at room temperature for 36 hours.

treatment_protocol: Rice leaf sheath pieces were placed in wire supports in order to avoid contact with the wet paper, and to hold the pieces horizontally flat for even inoculum distribution over the mid-vein. Spore suspension (1 X 105 spores/mL in gelatin solution) was injected in one end of the leaf sheath using a 1 mL pipet.

tag: Biotrophic invasive hyphae in rice sheath epidermal cells


title: Mycelia/Rice vs lesion biological rep 2.2


title: Mycelia/Rice vs lesion biological rep 3.1


title: NR-S1, primary tumor control (Cy5) vs. lung metastasis gamma 8 Gy (Cy3), replicate 1


title: NR-S1, primary tumor control (Cy5) vs. lung metastasis control (Cy3), replicate 1

description: Murine squamous cell carcinoma, NR-S1, was transplanted into the hind leg of C3H/HeMsNrs mice. The primary tumors were sampled at 1 week after the diameter of the tumor became 7.5mm, and metastatic tumors were sampled at 2 weeks after the diameter of the tumor became 7.5mm. The tumor cells were collected using the laser microdissection technique, and the expression profiles of the primary tumor and the metastatic tumors were compared using the two-color method.

source_name: NR-S1, lung metastasis, 2 weeks after 7.5 mm, clone 1

value: C3H/HeMsNrs, Gender:male, Tumor type:NR-S1 (squamous cell carcinoma), Tumor site:metastasic tumor (lung), Time:2 weeks after the diameter of the primary tumor had reached 7.5 mm, Irradiation:None


title: NR-S1, lung metastasis control (Cy5) vs. primary tumor control (Cy3), replicate 1

value: C3H/HeMsNrs, Gender:male, Tumor type:NR-S1 (squamous cell carcinoma), Tumor site:metastasic tumor (lung), Time:2 week after the diameter of the primary tumor had reached 7.5 mm, Irradiation:None


title: Lesion vs mycelia/Rice biological rep 3.4


title: Lesion vs mycelia/Rice biological rep 1.2


title: Mycelia/rice vs lesion biological rep 2.3

description:
This experiment was designed to compare gene expression
by biotrophic invasive hyphae in planta to gene expression
by mycelium in nutrient medium

scan_protocol: Slides were scanned on an Agilent G2565BA DNA microarray scanner, and the TIFF images extracted using the Agilent Feature Extraction software (version 8.5). The resultant .xml and .jpeg files were imported into Rosetta Resolver.

extract_protocol: Trizol method as specified by the manufacturers


title: mycelia/Ryce vs lesion biological rep 1.3


title: Lesion vs mycelia/Rice biological rep 3.3


title: Mycelia/Rice vs lesion biological rep 1.2


title: Lesion vs mycelia/rice biological rep 2.4


title: Mycelia/rice vs lesion biological rep 2.4


title: Lesion vs mycelia/rice biological rep 1.3


title: Mycelia/Rice vs lesion biological rep 1.4


title: lesion vs mycelia/rice biological rep 1.1


title: Mycelia/rice vs lesion biological rep 3.4


title: mycelia/Rice vs lesion biological rep 2.1


title: Lesion vs mycelia/rice biological rep 2.3


title: Lesion vs mycelia/rice biological rep 2.1


title: Lesion vs mycelia/rice biological rep 2.2


title: Lesion vs mycelia/rice biological rep 3.1


title: PAX9_rep6

status: Public on Apr 01 2009

first: Chaitanya

middle: R

last: Acharya

address: 203 Research Drive,Medical Sciences Research Building, Suite 433

department: Dept. of Surgery

description: Gene expression data from cell-lines transfected by PAX9.

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133 Plus 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

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

data_processing: The data were analyzed using Stratagene's ArrayAssist Enterprise using Affymetrix default analysis settings.

source_name: Transfectant cells overexpressing PAX9

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

extract_protocol: Total RNA from stable transfectant cells over-expressing individual transcription factors was extracted using the QiaShredder and Qiagen RNeasy Mini kit.

tag: Hygromycin-selected


title: Lesion vs mycelia/rice biological rep1.4


title: Lesion vs mycelia/rice biological rep 3.2


title: Mycelia/rice vs lesion biological rep 3.3

treatment_protocol: Sheaths inoculated with gelatin solution. An approximately 1 cm square piece of agar containing fungus was excised from the surface of an oatmeal agar plate and blended in 25 ml of 3,3,3 liquid medium (3g/L of glucose, 3g/L of casamino acids, and 3g/L of yeast extract). The blended mycelium was mixed with 225 ml of fresh medium in 500 ml flasks


title: TTF1_rep6

description: Gene expression data from cell-lines transfected by TTF1.

source_name: Transfectant cells overexpressing TTF1


title: NKX2-8_rep6

description: Gene expression data from cell-lines transfected by NKX2-8.

source_name: Transfectant cells overexpressing NKX2-8


title: NKX2-8_rep5

tag: Blasticidin-selected


title: TTF1_rep5


title: Mycelia/rice vs lesion biological rep 1.1


title: Control_rep6

description: Gene expression data from cell-lines not transfected with any transcription factor.

source_name: Empty vector control


title: PAX9_rep5


title: Control_rep5


title: TTF1_rep4


title: NKX2-8_rep4


title: PAX9_rep4


title: Control_rep4


title: TTF1_rep3

tag: puromycin-selected


title: NKX2-8_rep2


title: PAX9_rep2


title: NKX2-8_rep1


title: TTF1_rep1


title: Control_rep2


title: TTF1_rep2


title: Control_rep3


title: NKX2-8_rep3


title: PAX9_rep3


title: Control_rep1


title: PAX9_rep1


title: GM18500

status: Public on Mar 23 2009

city: Chicago

first: Eileen

last: Dolan

state: IL

address: 5841 S. Maryland

department: Medicine

institute: University of Chicago

description: Homo sapiens lymphoblastoid cell lines (30 CEPH trios and 30 Yoruban  trios) were purchased from Coriell Institute for Medical Reseach (Camden, NJ).

hyb_protocol: Approximately 5.5ug of labeled DNA target was hybridized to the Affymetrix GeneChip Human Exon 1.0 ST Array at 45° C for 16 hours per manufacturer's recommendation (see http://www.affymetrix.com/products/arrays/exon_application.affx for additional information).  Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: All samples were scanned on a GCS3000 Scanner (Affymetrix, Inc.).

data_processing: Expression arrays were analyzed using the Affymetrix PowerTools v1.8.6 (http://www.affymetrix.com/support/developer/powertools/index.affx). The start and end coordinates of all probes represented on the exon array were queried and determined against the human genome (hg18). The coordinates for all SNPs were then queried in the dbSNP database (release 129) (http://www.ncbi.nlm.nih.gov/projects/SNP) and used to identify probes harboring SNPs.  Of the ~1.4 million probesets on the exon array, ~288,400 contained at least one probe with a SNP. The probeset signal intensity files were filtered by removing those ~288,400 probes from the probesets harboring these known SNPs. Probe intensities were then background corrected and quantile normalized over all 176 samples. The data were then log2 transformed with a median polish. Gene-level expression of 17,879 transcript clusters was summarized using the RMA (robust multi-array average) method with signals generated on a core set (i.e. with RefSeq-supported annotation) of exons (~288,400 probesets). A transcript cluster or probeset was defined to be reliably expressed in LCLs if the log2 transformed expression signal was greater than 5 in at least 80% of the 176 samples. 10,796 of the 17,879 core transcript clusters met these criteria(15). To avoid annotation ambiguity, the final analysis dataset is comprised of 7,860 expressed transcript clusters (corresponding to 115,544 probesets, a minimum of 3 probesets for each transcript cluster) with unique gene annotations (based on NCBI Human Genome Build 34) as retrieved at the Affymetrix NetAffx Ananlysis Center (http://www.affymetrix.com/analysis/index.affx).

source_name: lymphoblastoid cell line

label_protocol: Ribosomal RNA was depleted from 1ug of total RNA using the RiboMinus Human/Mouse Transcriptome Isolation kit (Invitrogen Corp., Carlsbad, CA).  cDNA was generated using the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Inc., Santa Clara, CA) per manufacturer's instructions.  cDNA was fragmented and end labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix, Inc.).

growth_protocol: Lymphoblastoid cell lines were centrifuged at 400 × g to remove media and 5 mL fresh lymphoblastoid cell media (LCL media) containing RPMI 1640 (Mediatech)/1% l-glutamine (Mediatech) plus 20% FBS (HyClone Laboratories) for the initial passage and then passaged every 48 h with LCL medium and 15% FBS. Cell suspensions were transferred to 25 cm2 flasks and incubated at 37° C in a 90% humidified 5% CO2 atmosphere. Cell lines were maintained at a concentration of 3.5-4.0×105 cells/mL and harvested following the 4th passage, only if viability ≥ 85%.

extract_protocol: Lymphoblastoid cell line suspensions were spun at 400 × g for 5 min to remove media. Cell pellets were washed twice with ice-cold PBS and stored at -80° C. Total RNA was extracted using RNeasy Plus Kits according to the manufacturers protocol.

treatment_protocol: Each sample was collected while in exponential growth, all remained untreated.  Baseline expression data.

tag: Coriell cell line repository identifier

tag: Yoruban sample

tag: Gender

value: Male

tag: Associated family

tag: Family relationship

value: child


title: GM18515


title: GM18502

value: Female

value: mother


title: GM18506


title: GM18507

value: father


title: GM18503


title: GM18501


title: GM18516


title: GM12892

tag: CEPH sample

value: maternal grandmother


title: GM18517


title: GM07034

value: paternal grandfather


title: GM18508


title: GM18505


title: GM18504


title: GM12873

value: paternal grandmother


title: GM12814

value: maternal grandfather


title: GM12878


title: GM12875


title: GM12815


title: GM12872


title: GM12865


title: GM12813


title: GM12891


title: GM07029


title: GM12874


title: GM12812


title: GM12864


title: Cytoplasmic RNA from Human HepG2 cells

status: Public on Mar 24 2009

city: Santa Clara

first: Thomas

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

description: Sample purchased from Clontech, Inc. No further treatment or processing done.

hyb_protocol: Refer publications: Kapranov et al. Science 2007(Vol# 316. no. 5830,pp.1484-1488); ENCODE project consortium,Nature 2007 (Vol# 447, 799-816)

data_processing: Two technical replicates were hybridized for this experiment. The data from replicate arrays were quantile-normalized (Bolstad et al., 2003) and all arrays were scaled to a median array intensity of 330. The sliding window approach has not been used to estimate RNA abundance (signal which is listed in column #2). It was found by calculating the median of all pairwise average PM-MM values, where PM is a perfect match and MM is a mismatch. Transcribed regions (represented by probe's present/absent calls in column #3) were generated from the composite signal track by merging genomic positions to which probes are mapped. This merging was based on a 5% false positive rate cutoff in negative bacterial controls, a maximum gap (MaxGap) of 25 base-pairs and minimum run (MinRun) of 25 base-pairs. The columns #2 and #3 are obtained from analysis done on Human Genome hs.NCBIv36 or hg18 (UCSC).

molecule: cytoplasmic RNA

source_name: Human HepG2 cells

extract_protocol: See manufacturer's protocol for details

tag: Commercial Source

value: Clontech, Inc. Mountain View, CA (http://www.clontech.com/)


title: GM12802


title: GM07022


title: GM12753


title: GM12801


title: GM12763


title: GM12760


title: GM12707


title: GM12752


title: GM12740


title: GM12717


title: Total RNA from Human Prostate cells

scan_protocol: Refer publications: Kapranov et al. Science 2007(Vol# 316. no. 5830,pp.1484-1488); ENCODE project consortium,Nature 2007 (Vol# 447, 799-816)

source_name: Human Prostate cells


title: GM12264


title: GM12248


title: Total RNA from Human Fetal Kidney cells

source_name: Human Fetal Kidney cells

label_protocol: Refer publications: Kapranov et al. Science 2007(Vol# 316. no. 5830,pp.1484-1488); ENCODE project consortium,Nature 2007 (Vol# 447, 799-816)


title: Total RNA from Human HeLaS3 cells

source_name: Human HeLaS3 cells


title: GM12239


title: GM07019


title: GM12762


title: GM12249


title: Total RNA from Human Placenta cells

source_name: Human Placenta cells


title: GM12234


title: Total RNA from Human Testis cells

source_name: Human Testis cells


title: Total RNA from Human K562 cells

source_name: Human K562 cells


title: Total RNA from Human Brain Frontal Lobe cells

source_name: Human Brain Frontal Lobe cells


title: Cytoplasmic RNA from Human GM06990 cells

source_name: Human GM06990 cells


title: GM12761


title: Total RNA from Human Fetal Spleen cells

source_name: Human Fetal Spleen cells


title: Cytoplasmic RNA from Human fibroblast cells immortalized with hTert gene


title: Total RNA from Human Brain Hypothalamus cells

source_name: Human Brain Hypothalamus cells


title: GM12750


title: GM12155


title: GM12751


title: GM12146


title: GM12145


title: GM12154


title: Total RNA from Human Brain Hippocampus cells

source_name: Human Brain Hippocampus cells


title: Total RNA from Human Ovary cells

source_name: Human Ovary cells


title: Total RNA from Human Brain Cerebellum cells

source_name: Human Brain Cerebellum cells


title: GM12056


title: GM12043


title: GM12144


title: GM07000


title: GM12044


title: GM12006


title: GM12004


title: GM12156


title: GM11993


title: GM11994


title: GM06994


title: GM12005


title: GM11992


title: GM11882


title: GM12003


title: GM10863


title: GM11839


title: GM11881


title: GM11831


title: GM11829


title: GM11995


title: GM06993


title: GM11832


title: GM12057


title: GM11840


title: Total RNA from Human Fetal Thymus cells

source_name: Human Fetal Thymus cells


title: GM11830


title: GM10860


title: GM10861


title: GM10856


title: GM10859


title: GM10854


title: GM10851


title: GM10857


title: GM19240


title: GM10835


title: GM06991


title: GM19238


title: GM19239


title: GM19222


title: GM10838


title: GM19204


title: GM19202


title: GM19205


title: GM19211


title: GM19208


title: GM10831


title: GM19221


title: GM19223


title: GM19209


title: GM19210


title: GM19206


title: GM19203


title: GM10847


title: GM19193


title: GM10846


title: GM19194


title: GM19201


title: GM19173


title: GM19153


title: GM19172


title: GM10830


title: GM19161


title: GM07348


title: GM19140


title: GM19145


title: GM19160


title: GM19142


title: GM19154


title: GM19143


title: GM19171


title: GM19192


title: GM07357


title: GM19144


title: GM10839


title: GM19141


title: GM19137


title: GM19138


title: GM19139


title: GM19152


title: GM19131


title: GM19200


title: GM19130


title: GM19128


title: GM19119


title: GM19120


title: GM19127


title: GM19129


title: GM19159


title: GM19103


title: GM18872


title: GM19098


title: GM18870


title: GM18913


title: GM19093


title: GM18914


title: GM19099


title: GM18912


title: GM19094


title: GM19100


title: GM18863


title: GM07345


title: GM19092


title: GM19101


title: GM19102


title: GM19116


title: GM19132


title: GM18861


title: GM18862


title: GM07056


title: GM18859


title: GM18858


title: GM18860


title: GM18857


title: GM07055


title: GM18855


title: GM18523


title: GM18522