title: Olive_cultivar Chondrolia Chalkidikis_90days of stress_120mM NaCl replicate 4

description: CH_t_90s rep4

source_name: Olive cv. Chondrolia Chalkidikis roots 90days_120mM NaCl stress


title: Olive_cultivar Chondrolia Chalkidikis_90days of stress_120mM NaCl replicate 3

status: Public on Nov 20 2012

type: RNA

city: Chania

first: Maria

middle: E.

last: Manioudaki

address: Makedonias 1

department: Horticultural Genetics and Biotechnology

country: Greece

institute: MAICH

description: CH_t_90s rep3

hyb_protocol: Fluorescent samples were combined and purified using the PureLink™ PCR purification System. The only modification was the use of 20μl Low temp Hybridization buffer as elution buffer. The probe was supplemented with 3.5 μl of 5 mg/ml Salmon sperm DNA and 2 μl of yeast tRNA. The mixture was heated at 60oC for 5 minutes and was kept at 45oC before hybridization. The probes were placed onto the array; the slides in a sealed hybridization cassette and submerged in a 43oC water bath for 18 hours. The slides were then placed in washing solution 1 (1X SSC, 0.03% SDS) and then transferred to washing solution 2 (0.2X SSC) for 5 min with agitation followed by washing solution 3 (0.05X SSC).

scan_protocol: Microarrays were scanned with an Axon microarray scanner (model GenePix 4000B).

data_processing: The scanned images were analyzed using GenePix Pro 6.0 software. Spots were flagged as ‘not found’, ‘absent’ or ‘bad’.  The default local background subtraction method was used. Feature data were extracted from the raw images as GenePix Results files (.gpr) and converted to TIGR MultiExperiment Viewer (.mev) files using the ExpressConverter V2.1 tool implemented in the TM4 microarray software suite.  The Integrated Intensity Value (IIV) for each spot was subsequently used as input for the normalization pipeline in MIDAS V2.21 software which included the following steps (1) locally weighted scatterplot smoothing regression (LOWESS) normalization in block mode (2) in-slide replicate analysis and (3) low-intensity filtering that removes intensity values <10000. Low-quality array elements were eliminated by applying background checking for both channels with a signal/noise threshold of 2.0 and usage of flags for both channels. One bad tolerance policy parameter was set to generous.

label: Alexa 647

molecule: total RNA

organism: Olea europaea

label_protocol: 15 μg of intact total RNA were labeled with SuperScript™ Plus Direct cDNA Labeling System (Invitrogen) using Alexa Fluor®-labeled nucleotides

growth_protocol: One year-old, self-rooted trees of Olea europaea L., cv. Chondrolia Chalkidikis obtained from a commercial nursery and grown under identical conditions were transplanted in plastic bags containing a 1:1 mixture of perlite:sand. The young trees were irrigated daily with 150ml of half-strength Hoagland solution for one month and 35 of those of similar growth were selected for the salinity experiment while another 35 for the un-treated control. Totally 70 young trees per cultivar were used for the experiment.

extract_protocol: Four young trees were used to collect root tissue at each point of treatment. The root tissue was washed repeatedly with deionised water, sterilized with 0.5% sodium hypochloride, immediately ground with liquid nitrogen and stored at a -80°C freezer. Total RNA was extracted according to the method of Bachem et al., 1998 and concentrated using the NucleoSpin® RNA Clean-up XS kit.

treatment_protocol: Plants were irrigated daily with 150ml of half-strength Hoagland solution containing in addition 0 (control) and 120 mM/l NaCl for 15, 45, 90 days through salt stress experiment and with half strength Hoagland solution for 15 and 45 days through post-stress period.

tag: cultivar

value: Chondrolia Chalkidikis (salt sensitive)

tag: tissue

value: root


title: Olive_cultivar Chondrolia Chalkidikis_90days of stress_120mM NaCl replicate 2

description: CH_t_90s rep2

label: Alexa 555


title: 071-046_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo.CEL

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

country: USA

institute: Seattle Biomedical Research Institute

description:
probe group file: BrainArray version 9: HsEx10stv2_Hs_ENTREZG
meta-probeset file: BrainArray version 9: HsEx10stv2_Hs_ENTREZG

hyb_protocol: Samples were hybridized according to the Whole Transcript Sense Target Labeling protocol: *Heat cocktails at 99° for 5 minutes, 42° for 5 minutes, and then centrifuged at 13,200g for 1 minute. *Transfer 200uL of hyb solution to each array. *Hybridize 16 hours at 45° at 60rpm. *Wash and stain using fluidics protocol FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Microarrays were normalized at the gene level using the BrainArray custom CDF (Entrez Gene, Version 9) for probeset definitions and RMA as implemented in the justRMA function of the Bioconductor package affy for background adjustment, quantile normalization and summarization.

label: biotin

organism: Homo sapiens

source_name: PBMC obtained after in vivo vaccination for varying times with MRKAd5/HIV

label_protocol: Total RNA samples were labeled as described in the Whole Transcript Sense Target Labeling protocol (Affymetrix)

growth_protocol: PBMC from healthy Ad5-seronegative individuals were in RPMI containing 10% FCS.

extract_protocol: Cells were frozen in RNAprotect cell reagent (Qiagen) for RNA purification.

treatment_protocol: PBMC were stimulated with 20,000 viral particles/cell of MRKAd5 empty vector or GTS buffer (mock)  for 24hrs in vitro.

tag: human subject anonymized id

tag: pre-existing serum ad5 neutralizing antibody titer (merck assay)

tag: pre-existing serum ad5 neutralizing antibody titer class

tag: time post vaccination or treatment

tag: vaccine or treatment

tag: in vivo or in vitro

value: in vivo


title: 071-052_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo.CEL


title: 071-044_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo.CEL


title: 071-050_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo.CEL


title: Olive_cultivar Chondrolia Chalkidikis_45days of stress_120mM NaCl replicate 4

description: CH_t_45s rep4

source_name: Olive cv. Chondrolia Chalkidikis roots 45days_120mM NaCl stress


title: Olive_cultivar Chondrolia Chalkidikis_45days of stress_120mM NaCl replicate 3

description: CH_t_45s rep3


title: 071-044_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo.CEL


title: Olive_cultivar Chondrolia Chalkidikis_45days of stress_120mM NaCl replicate 2

description: CH_t_45s rep2


title: 071-015_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo.CEL


title: 071-025_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo.CEL


title: 071-035_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo.CEL


title: 071-025_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo.CEL


title: Olive_cultivar Chondrolia Chalkidikis_15days of stress_120mM NaCl replicate 4

description: CH_t_15s rep4

source_name: Olive cv. Chondrolia Chalkidikis roots 15days_120mM NaCl stress


title: Olive_cultivar Chondrolia Chalkidikis_90days of stress_120mM NaCl replicate 1

description: CH_t_90s rep1


title: Olive_cultivar Chondrolia Chalkidikis_15days of stress_120mM NaCl replicate 3

description: CH_t_15s rep3


title: 071-015_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo.CEL


title: 071-056_Ad5Titer_111_time_072hr_vaccine_MRKAd5_exp_vivo

growth_protocol: Not applicable

extract_protocol: Blood was collected immediately before vaccination and at 4-6, 24, 72, and 168 hours post-vaccination. PBMC RNA was extracted using the RNeasy Protect Cell protocol (Qiagen)

treatment_protocol: At the start of the trial (Day 0), all volunteers were intramuscularly vaccinated with 1.5x10^10 genomes of the MRKAd5/HIV vaccine


title: Olive_cultivar Chondrolia Chalkidikis_15days of stress_120mM NaCl replicate 2

description: CH_t_15s rep2


title: Olive_cultivar Chondrolia Chalkidikis_15days of stress_120mM NaCl replicate 1

description: CH_t_15s rep1


title: Olive_cultivar Chondrolia Chalkidikis_45days of stress_120mM NaCl replicate 1

description: CH_t_45s rep1


title: Olive_cultivar Chondrolia Chalkidikis_45days of post-stress_control replicate 4

description: CH_c_45ps rep4

source_name: Olive cv. Chondrolia Chalkidikis roots 45days post-stress_control


title: CUP patient 56

city: Osaka-Sayama

first: Yoshihiko

last: Fujita

address: 377-2 Ohno-Higashi

country: Japan

institute: Kinki university School of Medicine

hyb_protocol: IVT products were magnetic-bead purified, frangmented, and hybridized onto Affymetrix U133 plus 2.0 GeneChip at 45° C for 16 h.

scan_protocol: Scanner in an Affymetrix GeneChip Scanner 3000 7G (Santa Clara, CA).

data_processing: Data extraction was done by the Affymetrix GCOS software v1.4.

source_name: metastatic lesion

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol.

extract_protocol: The mRNA extraction was done using the Isogen protocol

value: lymph node

tag: disease state

value: cancer of unknown primary


title: Olive_cultivar Chondrolia Chalkidikis_45days of post-stress_control replicate 2

description: CH_c_45ps rep2


title: 071-056_Ad5Titer_111_time_024hr_vaccine_MRKAd5_exp_vivo


title: Olive_cultivar Chondrolia Chalkidikis_45days of post-stress_control replicate 1

description: CH_c_45ps rep1


title: CUP patient 53


title: CUP patient 59


title: 071-056_Ad5Titer_111_time_168hr_vaccine_MRKAd5_exp_vivo


title: CUP patient 52


title: CUP patient 60


title: 071-056_Ad5Titer_111_time_006hr_vaccine_MRKAd5_exp_vivo


title: CUP patient 49


title: CUP patient 54


title: 071-056_Ad5Titer_111_time_000hr_vaccine_MRKAd5_exp_vivo


title: CUP patient 51


title: CUP patient 57


title: CUP patient 50


title: 071-035_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo.CEL


title: Olive_cultivar Chondrolia Chalkidikis_15days of post-stress_control replicate 4

description: CH_c_15ps rep4

source_name: Olive cv. Chondrolia Chalkidikis roots 15days post-stress_control


title: Olive_cultivar Chondrolia Chalkidikis_45days of post-stress_control replicate 3

description: CH_c_45ps rep3


title: CUP patient 55


title: CUP patient 45


title: CUP patient 48


title: CUP patient 47


title: CUP patient 42


title: Olive_cultivar Chondrolia Chalkidikis_15days of post-stress_control replicate 3

description: CH_c_15ps rep3


title: Olive_cultivar Chondrolia Chalkidikis_15days of post-stress_control replicate 2

description: CH_c_15ps rep2


title: Olive_cultivar Chondrolia Chalkidikis_15days of post-stress_control replicate 1

description: CH_c_15ps rep1


title: Olive_cultivar Chondrolia Chalkidikis_90days of stress_control replicate 4

description: CH_c_90s rep4

source_name: Olive cv. Chondrolia Chalkidikis roots 90days stress_control


title: Olive_cultivar Chondrolia Chalkidikis_90days of stress_control replicate 3

description: CH_c_90s rep3


title: Olive_cultivar Chondrolia Chalkidikis_90days of stress_control replicate 2

description: CH_c_90s rep2


title: CUP patient 39


title: CUP patient 36


title: Olive_cultivar Chondrolia Chalkidikis_90days of stress_control replicate 1

description: CH_c_90s rep1


title: CUP patient 44


title: CUP patient 33


title: CUP patient 46


title: CUP patient 35


title: CUP patient 40


title: CUP patient 41


title: CUP patient 37


title: CUP patient 38

value: ascites/hydrothorax


title: Olive_cultivar Chondrolia Chalkidikis_45days of stress_control replicate 3

description: CH_c_45s rep3

source_name: Olive cv. Chondrolia Chalkidikis roots 45days stress_control


title: CUP patient 31


title: CUP patient 34


title: CUP patient 32


title: CUP patient 43


title: CUP patient 29


title: CUP patient 26


title: CUP patient 27


title: CUP patient 28


title: CUP patient 30


title: CUP patient 25


title: Olive_cultivar Chondrolia Chalkidikis_45days of stress_control replicate 2

description: CH_c_45s rep2


title: Olive_cultivar Chondrolia Chalkidikis_45days of stress_control replicate 1

description: CH_c_45s rep1


title: CUP patient 23


title: CUP patient 22


title: CUP patient 20


title: CUP patient 24


title: Olive_cultivar Chondrolia Chalkidikis_45days of stress_control replicate 4

description: CH_c_45s rep4


title: Olive_cultivar Chondrolia Chalkidikis_15days of stress_control replicate 3

description: CH_c_15s rep3

source_name: Olive cv. Chondrolia Chalkidikis roots 15days stress_control


title: Olive_cultivar Chondrolia Chalkidikis_15days of stress_control replicate 4

description: CH_c_15s rep4


title: CUP patient 21


title: Olive_cultivar Chondrolia Chalkidikis_15days of stress_control replicate 2

description: CH_c_15s rep2


title: CUP patient 19


title: CUP patient 18


title: CUP patient 17


title: Olive_cultivar Kalamon_45days of post-stress_120mM NaCl replicate 4

description: KA_t_45ps rep4

hyb_protocol: Fluorescent samples were combined and purified using the PureLink™ PCR purification System. The only modification was the use of 20μl Low temp Hybridization buffer as elution buffer. The probe was supplemented with 3.5 μl of 5 mg/ml Salmon sperm DNA and 2 μl of yeast tRNA. The mixture was heated at 60C for 5 minutes and was kept at 45C before hybridization. The probes were placed onto the array; the slides in a sealed hybridization cassette and submerged in a 43oC water bath for 18 hours. The slides were then placed in washing solution 1 (1X SSC_0.03% SDS) and then transferred to washing solution 2 (0.2X SSC) for 5 min with agitation followed by washing solution 3 (0.05X SSC).

data_processing: The scanned images were analyzed using GenePix Pro 6.0 software. Spots were flagged as 'not found', 'absent' or 'bad'.  The default local background subtraction method was used. Feature data were extracted from the raw images as GenePix Results files (.gpr) and converted to TIGR MultiExperiment Viewer (.mev) files using the ExpressConverter V2.1 tool implemented in the TM4 microarray software suite.  The Integrated Intensity Value (IIV) for each spot was subsequently used as input for the normalization pipeline in MIDAS V2.21 software which included the following steps (1) locally weighted scatterplot smoothing regression (LOWESS) normalization in block mode (2) in-slide replicate analysis and (3) low-intensity filtering that removes intensity values <10000. Low-quality array elements were eliminated by applying background checking for both channels with a signal/noise threshold of 2.0 and usage of flags for both channels. One bad tolerance policy parameter was set to generous.

source_name: Olive cv. Kalamon roots 45days_post-120mM NaCl-stress

label_protocol: 15 μg of intact total RNA were labeled with SuperScript™ Plus Direct cDNA Labeling System (Invitrogen) using Alexa Fluor®-labeled nucleotides.

growth_protocol: One year-old_self-rooted trees of Olea europaea L._cvs. Kalamon and Chondrolia Chalkidikis obtained from a commercial nursery and grown under identical conditions were transplanted in plastic bags containing a 1:1 mixture of perlite:sand. The young trees were irrigated daily with 150ml of half-strength Hoagland solution for one month and 35 of those of similar growth were selected for the salinity experiment while another 35 for the un-treated control. Totally 70 young trees per cultivar were used for the experiment.

extract_protocol: Four young trees were used to collect root tissue at each point of treatment. The root tissue was washed repeatedly with deionised water_sterilized with 0.5% sodium hypochloride_immediately ground with liquid nitrogen and stored at a -80°C freezer. Total RNA was extracted according to the method of Bachem et al._1998 and concentrated using the NucleoSpin® RNA Clean-up XS kit.

value: Kalamon (salt-tolerant)


title: CUP patient 12


title: CUP patient 58


title: Olive_cultivar Kalamon_45days of post-stress_120mM NaCl replicate 2

description: KA_t_45ps rep2


title: Olive_cultivar Kalamon_45days of post-stress_120mM NaCl replicate 3

description: KA_t_45ps rep3


title: Olive_cultivar Chondrolia Chalkidikis_15days of stress_control replicate 1

description: CH_c_15s rep1


city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_RB grown in axenic media + rifampicin rep 3

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. MAS5.0 signal intensity

organism: Chlamydia trachomatis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Chlamydia trachomatis serovar L2 (LGV 434) was propagated in HeLa 229 cells and purified by Renografin density gradient centrifugation.  RBs were isolated 14-16 h post infection while EBs were isolated 43-45 h post infection.

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

treatment_protocol: EBs and RBs were treated with axenic medium in the presence or absence of rifampicin for 3 hours.

value: chlamydial reticulate bodies


title: CUP patient 13


title: CUP patient 11


description: Gene expression data from_RB grown in axenic media + rifampicin rep 4


title: Olive_cultivar Kalamon_45days of post-stress_120mM NaCl replicate 1

description: KA_t_45ps rep1


title: CUP patient 15


title: CUP patient 16


title: CUP patient 14


description: Gene expression data from_RB grown in axenic media + rifampicin rep 2


title: Olive_cultivar Kalamon_15days of post-stress_120mM NaCl replicate 4

description: KA_t_15ps rep4

source_name: Olive cv. Kalamon roots 15days_post-120mM NaCl-stress


title: CUP patient 9


title: RB grown in axenic media rep 4

description: Gene expression data from_RB grown in axenic media rep 4

source_name: RB grown in axenic media rep 4


description: Gene expression data from_RB grown in axenic media + rifampicin rep 1


title: CUP patient 2


title: CUP patient 8


title: CUP patient 6


title: CUP patient 4


title: Olive_cultivar Kalamon_15days of post-stress_120mM NaCl replicate 3

description: KA_t_15ps rep3


title: RB grown in axenic media rep 2

description: Gene expression data from_RB grown in axenic media rep 2

source_name: RB grown in axenic media rep 2


title: CUP patient 10


title: CUP patient 5


title: CUP patient 7


title: CUP patient 3


title: RB grown in axenic media rep 3

description: Gene expression data from_RB grown in axenic media rep 3

source_name: RB grown in axenic media rep 3


title: Olive_cultivar Kalamon_15days of post-stress_120mM NaCl replicate 2

description: KA_t_15ps rep2


title: CUP patient 1


title: AMKL patient sample SJAMLM7016

city: Memphis

first: Tanja

middle: Andrea

last: Gruber

state: TN

address: 262 Danny Thomas Place

department: Oncology

institute: St. Jude Childrens Research Hospital

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7016.CEL

hyb_protocol: cDNA was fragmented by digestion with Uracil DNA glycosylase and apurinic/apyrimidinic endonuclease I. After fragmentation, 5 microgram of cDNA was hybridized for 16 hr at 45C on each array.  GeneChips were washed and stained automatically in the Affymetrix Fluidics Station 450 using the FS450_0001 protocol.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing:
Gene expression profiles were obtained by applying the Robust Multichip Average (RMA) implementation included in the Affymetrix Power Tools (APT).
probe group file: HuEx-1_0-st-v2.pgf
meta-probeset file: modified HuEx-1_0-st-v2.r2.dt1.hg18.core.mps with PTCH1 gene included

source_name: RNA extracted from diagnostic leukemic blasts of acute myelogenous leukemia

label_protocol: Biotinylated sense target cDNA was prepared from 100 ng of total RNA according to the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix P/N 701880 Rev. 2, 2005)

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from AML cases

extract_protocol: Trizol

value: acute myelogenous leukemia

tag: cell type

value: tumor cells (diagnostic leukemic blasts)

tag: subtype

tag: sequence mutations

value: GATA1:T101fs het, RB1R445* het

tag: cytogenetics


title: Olive_cultivar Kalamon_90days of stress_120mM NaCl replicate 4

description: KA_t_90s rep4

source_name: Olive cv. Kalamon roots 90days_120mM NaCl stress


title: AMKL patient sample SJAMLM7013

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7013.CEL

tag: cryptic fusions


title: Olive_cultivar Kalamon_15days of post-stress_120mM NaCl replicate 1

description: KA_t_15ps rep1


title: RB grown in axenic media rep 1

description: Gene expression data from_RB grown in axenic media rep 1

source_name: RB grown in axenic media rep 1


title: AMKL patient sample SJAMLM7014

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7014.CEL

value: Data not available


title: Olive_cultivar Kalamon_90days of stress_120mM NaCl replicate 2

description: KA_t_90s rep2


title: Olive_cultivar Kalamon_90days of stress_120mM NaCl replicate 1

description: KA_t_90s rep1


title: AMKL patient sample SJAMLM7012, technical replicate of AMKL patient sample M7-#2

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7012.CEL


title: AMKL patient sample SJAMLM7015

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7015.CEL


description: Gene expression data from_EB grown in axenic media + rifampicin rep 2

value: chlamydial elementary bodies


title: AMKL patient sample SJAMLM7010

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7010.CEL


title: AMKL patient sample SJAMLM7007

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7007.CEL

value: CBFA2T3-GLIS2 / GRB10-SDK1


title: Olive_cultivar Kalamon_45days of stress_120mM NaCl replicate 4

description: KA_t_45s rep4

source_name: Olive cv. Kalamon roots 45days_120mM NaCl stress


title: AMKL patient sample SJAMLM7008

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7008.CEL

value: KRASG12D (subclonal)


title: Olive_cultivar Kalamon_45days of stress_120mM NaCl replicate 3

description: KA_t_45s rep3


title: AMKL patient sample SJAMLM7009

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7009.CEL

value: JAK1L783F het


title: AMKL patient sample SJAMLM7006

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7006.CEL


title: AMKL patient sample SJAMLM7011

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7011.CEL

value: MPLS505N (subclonal)


description: Gene expression data from_EB grown in axenic media + rifampicin rep 3


title: AMKL patient sample SJAMLM7003

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7003.CEL


description: Gene expression data from_EB grown in axenic media + rifampicin rep 4


title: AMKL patient sample PML-#7

description:
RNA extracted from tumor cells obtained at diagnosis in childhood ALL with PML-RARA rearrangement
AML-Exon1.0ST-PML-#7.CEL

tag: batch

value: batch in year 2007

value: PML


title: AMKL patient sample SJAMLM7002

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7002.CEL

value: GATA1:D65Afs homo, JAK2V617F (subclonal), MPLS505N het


title: Olive_cultivar Kalamon_45days of stress_120mM NaCl replicate 2

description: KA_t_45s rep2

value: root


title: EB grown in axenic media rep 1

description: Gene expression data from_EB grown in axenic media rep 1

source_name: EB grown in axenic media rep 1


title: AMKL patient sample SJAMLM7005, technical replicate of AMKL patient sample M7-#6

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-SJAMLM7005.CEL

value: JAK2V617F het, NRASQ61R (subclone)


title: EB grown in axenic media rep 2

description: Gene expression data from_EB grown in axenic media rep 2

source_name: EB grown in axenic media rep 2


title: carry over of EB rep 4

description: Gene expression data from_carry over of EB rep 4

source_name: carry over of EB rep 4


title: AMKL patient sample PML-#6

description:
RNA extracted from tumor cells obtained at diagnosis in childhood ALL with PML-RARA rearrangement
AML-Exon1.0ST-PML-#6.CEL

value: FLT3: Y591-L601dup (10aa, mut<wt)


title: carry over of EB rep 3

description: Gene expression data from_carry over of EB rep 3

source_name: carry over of EB rep 3


title: AMKL patient sample N-#18

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-N-#18.CEL

value: Other

value: CEBPA:R35GfsX159 homo


title: Olive_cultivar Kalamon_45days of stress_120mM NaCl replicate 1

description: KA_t_45s rep1

value: Kalamon (salt-tolerant)


title: carry over of EB rep 2

description: Gene expression data from_carry over of EB rep 2

source_name: carry over of EB rep 2


title: AMKL patient sample N-#16

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-N-#16.CEL

value: acute myelogenous leukemia

value: tumor cells (diagnostic leukemic blasts)

value: NRAS:G13D / FLT3:D593-Y599dup / MLL-PTD


title: AMKL patient sample N-#12

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-N-#12.CEL


title: Olive_cultivar Kalamon_15days of stress_120mM NaCl replicate 4

description: KA_t_15s rep4

source_name: Olive cv. Kalamon roots 15days_120mM NaCl stress


title: Olive_cultivar Kalamon_15days of stress_120mM NaCl replicate 2

description: KA_t_15s rep2


title: Olive_cultivar Kalamon_15days of stress_120mM NaCl replicate 1

description: KA_t_15s rep1


title: Olive_cultivar Kalamon_45days of post-stress_control replicate 4

description: KA_c_45ps rep4

source_name: Olive cv. Kalamon roots 45days post-stress_control


title: AMKL patient sample N-#10

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-N-#10.CEL

value: CEBPA:V314STOP / FLT3:V592-R607dup (15aa, mut<wt)


title: Olive_cultivar Kalamon_45days of post-stress_control replicate 2

description: KA_c_45ps rep2


title: carry over of EB rep 1

description: Gene expression data from_carry over of EB rep 1

source_name: carry over of EB rep 1

value: chlamydial elementary bodies


title: AMKL patient sample misc-#7

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-misc-#7.CEL


title: AMKL patient sample misc-#6

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-misc-#6.CEL


title: AMKL patient sample N-#11

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-N-#11.CEL

value: FLT3:D593-F612dup (19aa, mut=wt)


title: High fat diet diet group, Time: 7 weeks, mouse number 6

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

description: Gene expression data from liver isolated from wild-type C57BL-6 male mice. High-fat diet group. Time: 7 weeks.

hyb_protocol: Samples were hybridized for 16 h at 45ºC onto the GeneChip® Mouse Gene 1.0 ST. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The CEL files were used to extract and normalize the data using Robust Multichip Average (RMA) implemented with the algorithm RMA Sketch for 1.0 ST arrays in the GeneChip Expression Console software version 1.1.2 (Affymetrix).

organism: Mus musculus

source_name: Liver isolated from wild-type C57BL-6 male mice. High-fat diet group. Time: 7 weeks.

label_protocol: RNA was processed according to the GeneChip® Whole Transcript (WT) Sense Target Labeling protocol (Affymetrix, Santa Clara, CA, USA). Amplified sense single-strand DNA was obtained using the Ambion® WT Expression Kit (Life Technologies). DNA was fragmented and labeled with the WT terminal Labeling kit.

growth_protocol: Mice livers were rapidly removed after the animals sacrifice, rinsed and kept in RNA Later (Qiagen, Madrid, Spain) (Ref.74134) at –80 °C prior to RNA isolation

extract_protocol: Total RNA was isolated from the mice livers using the RNeasy Plus Mini Kit de (Qiagen, Madrid, Spain) (Ref.74134) following the manufacturer recommendations. RNA was eluted in RNAse free water, aliquoted and stored at –80ºC. Isolated RNA was quantified using the NanoDrop ND-1000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality of the resulting RNA was determined by using the Experion RNA HighSens Bioanalyzer (Bio-Rad Laboratories, Inc.).

treatment_protocol: Livers were removed after 7 weeks of supplementation from miced fed: 1) a standard diet (SD), n=5 arrays (5 male mice); 2) a high-fat diet (HFD), n=5 arrays (5 male mice); 3) a standard diet plus a daily dose of the probiotic (1×109 CFU B. pseudocatenulatum CECT 7765) (SD+P), n=5 arrays (5 male mice); 4) a high-fat diet plus a daily dose of the probiotic (1×109 CFU B. pseudocatenulatum CECT 7765) (HFD+P), n=5 arrays (5 male mice).

tag: strain

tag: genotype/variation

value: wild-type

tag: diet

value: High-fat diet

value: liver


title: AMKL patient sample N-#5

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-N-#5.CEL

value: batch in year 2007

value: CEBPA:M15IfsX138 (not in GL)


title: AMKL patient sample N-#9

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-N-#9.CEL


title: High fat diet diet group, Time: 7 weeks, mouse number 5

tag: tissue


title: Olive_cultivar Kalamon_45days of post-stress_control replicate 1

description: KA_c_45ps rep1

tag: cultivar

value: root


title: AMKL patient sample misc-#3

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-misc-#3.CEL


title: AMKL patient sample N-#6

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-N-#6.CEL

value: CEBPA:H24AfsX103, S28N, R306_N307insL (all not in GL) / NRAS:G12D


title: AMKL patient sample misc-#2

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-misc-#2.CEL

value: CEPBA:G35RfsX123 (GL), S191-H192dup (GL)


title: High fat diet diet group, Time: 7 weeks, mouse number 8


title: AMKL patient sample misc-#23

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-misc-#23.CEL

value: Other


title: AMKL patient sample misc-#1

description:
RNA extracted from tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement
AML-Exon1.0ST-misc-#1.CEL

value: MLL


title: High fat diet diet plus probiotic group, Time: 7 weeks, mouse number 8

description: Gene expression data from liver isolated from wild-type C57BL-6 male mice. High-fat diet plus probiotic group. Time: 7 weeks.

source_name: Liver isolated from wild-type C57BL-6 male mice. High-fat diet plus probiotic group. Time: 7 weeks.

value: High-fat diet plus probiotic


title: AMKL patient sample misc-#9

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-misc-#9.CEL

value: acute myelogenous leukemia

value: CEPBA:P23QfsX80 (GL), M310TfsX38 (not in GL)


title: AMKL patient sample M7-#8

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-M7-#8.CEL

value: tumor cells (diagnostic leukemic blasts)

value: unknown (not sequenced); *Due to insufficient specimen, M7-#05/M7-08 did not undergo sequencing or CBFA2T3-GLIS2 RT-PCR.


title: AMKL patient sample N-#8

description:
RNA extracted from B-precursor ALL with miscellaneous or Normal karyotype
AML-Exon1.0ST-N-#8.CEL


title: Olive_cultivar Kalamon_15days of post-stress_control replicate 4

description: KA_c_15ps rep4

source_name: Olive cv. Kalamon roots 15days post-stress_control

value: Kalamon (salt-tolerant)


title: Olive_cultivar Kalamon_15days of post-stress_control replicate 3

description: KA_c_15ps rep3


title: High fat diet diet group, Time: 7 weeks, mouse number 1


title: High fat diet diet group, Time: 7 weeks, mouse number 2


title: AMKL patient sample MLL-#9

description:
RNA extracted from tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement
AML-Exon1.0ST-MLL-#9.CEL


title: AMKL patient sample M7-#6, technical replicate of AMKL patient sample SJAMLM7005

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-M7-#6.CEL


title: Olive_cultivar Kalamon_15days of post-stress_control replicate 1

description: KA_c_15ps rep1


title: High fat diet diet plus probiotic group, Time: 7 weeks, mouse number 6


title: AMKL patient sample M7-#2

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-M7-#2.CEL


title: Olive_cultivar Kalamon_90days of stress_control replicate 4

description: KA_c_90s rep4

source_name: Olive cv. Kalamon roots 90days stress_control


title: AMKL patient sample i16-#8

description:
RNA extracted from tumor cells obtained at diagnosis in childhood ALL with inv 16(p13;q22) translocation
AML-Exon1.0ST-i16-#8.CEL

value: CBF


title: AMKL patient sample i16-#4

description:
RNA extracted from tumor cells obtained at diagnosis in childhood ALL with inv 16(p13;q22) translocation
AML-Exon1.0ST-i16-#4.CEL


title: AMKL patient sample M7-#5

description:
RNA extracted from tumor cells obtained at diagnosis in childhood Acute megakaryoblastic leukemia
AML-Exon1.0ST-M7-#5.CEL


title: High fat diet diet plus probiotic group, Time: 7 weeks, mouse number 5

value: wild-type


title: AMKL patient sample AE-#10

description:
RNA extracted from tumor cells obtained at diagnosis in childhood ALL with AML1-ETO rearrangement
AML-Exon1.0ST-AE-#10.CEL


title: Olive_cultivar Kalamon_45days of stress_control replicate 4

description: KA_c_45s rep4

source_name: Olive cv. Kalamon roots 45days stress_control


title: Olive_cultivar Kalamon_90days of stress_control replicate 2

description: KA_c_90s rep2


title: Olive_cultivar Kalamon_90days of stress_control replicate 1

description: KA_c_90s rep1


title: AMKL patient sample M7-#2, technical replicate of AMKL patient sample SJAMLM7012

description:
RNA extracted from tumor cells obtained at diagnosis in childhood ALL with AML1-ETO rearrangement
AML-Exon1.0ST-AE-#2.CEL

source_name: RNA extracted from diagnostic leukemic blasts of acute myelogenous leukemia


title: AMKL patient sample AE-#6

description:
RNA extracted from tumor cells obtained at diagnosis in childhood ALL with AML1-ETO rearrangement
AML-Exon1.0ST-AE-#6.CEL

value: NRAS:G12D / MLL-PTD


title: High fat diet diet plus probiotic group, Time: 7 weeks, mouse number 4

value: liver


title: AMKL patient sample AE-#1

description:
RNA extracted from tumor cells obtained at diagnosis in childhood ALL with AML1-ETO rearrangement
AML-Exon1.0ST-AE-#1.CEL

value: batch in year 2007

value: NRAS:G13D, G12


title: Olive_cultivar Kalamon_45days of stress_control replicate 3

description: KA_c_45s rep3

value: root


title: Standard diet group, Time: 7 weeks, mouse number 5

description: Gene expression data from liver isolated from wild-type C57BL-6 male mice. Standard diet group. Time: 7 weeks.

source_name: Liver isolated from wild-type C57BL-6 male mice. Standard diet group. Time: 7 weeks.

value: Standard diet


title: High fat diet diet plus probiotic group, Time: 7 weeks, mouse number 2


title: Standard diet group, Time: 7 weeks, mouse number 6


title: Standard diet group, Time: 7 weeks, mouse number 8


title: Olive_cultivar Kalamon_45days of stress_control replicate 2

description: KA_c_45s rep2


title: Olive_cultivar Kalamon_15days of stress_control replicate 4

description: KA_c_15s rep4

source_name: Olive cv. Kalamon roots 15days stress_control


title: Standard diet group, Time: 7 weeks, mouse number 1


title: Standard diet group, Time: 7 weeks, mouse number 3


title: Olive_cultivar Kalamon_15days of stress_control replicate 2

description: KA_c_15s rep2


title: Olive_cultivar Kalamon_15days of stress_control replicate 3

description: KA_c_15s rep3


title: Olive_cultivar Kalamon_15days of stress_control replicate 1

description: KA_c_15s rep1


title: Standard diet plus probiotic group, Time: 7 weeks, mouse number 7

description: Gene expression data from liver isolated from wild-type C57BL-6 male mice. Standard diet plus probiotic group. Time: 7 weeks.

source_name: Liver isolated from wild-type C57BL-6 male mice. Standard diet plus probiotic group. Time: 7 weeks.

value: Standard diet plus probiotic


title: Standard diet plus probiotic group, Time: 7 weeks, mouse number 6


title: Standard diet plus probiotic group, Time: 7 weeks, mouse number 2


title: Standard diet plus probiotic group, Time: 7 weeks, mouse number 5


title: Standard diet plus probiotic group, Time: 7 weeks, mouse number 3


title: Olive_cultivar Kalamon_45days of stress_control replicate 1

description: KA_c_45s rep1


title: Ifnar1 Ifngr1_mock_rep3

status: Public on Nov 19 2012

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

hyb_protocol: Pooled reference and sample hybridized in 3x SSC/0.2% SDS as per standard protocols for spotted array hybridization

scan_protocol: Molecular Devices Genepix 4000B scanner at 5 um resolution

source_name: pooled reference amplified RNA from combination of universal mouse reference and samples

label_protocol: 4 ug of aRNA coupled to Cy5 (or Cy3 for common pooled reference aRNA) as per standard protocols

extract_protocol: Blood was harvested by cardiac puncture after euthanasia.  Total RNA was extracted with the Ambion RiboPure Blood kit and amplified with the Ambion Aminoallyl MessageAmp II kit.

treatment_protocol: C57BL/6 mice were infected with 10^6 erythrocytes infected with P. chabaudi or mock-infected with equivalent uninfected erythrocytes

tag: sample type

source_name: Amplified total RNA from whole blood isolated 24h post-treatment from mock-treated Ifnar1 Ifngr1 knockout mice

tag: genotype

value: Ifnar1 Ifngr1 KO

tag: infection status

value: Mock

value: whole blood

tag: genetic background


title: Ifnar1 Ifngr1_Pc_rep4

value: pooled reference amplified RNA from combination of universal mouse reference and samples

source_name: Amplified total RNA from whole blood isolated 24h post-treatment from P. chabaudi-infected Ifnar1 Ifngr1 knockout mice

value: P. chabaudi


title: Stat1_mock_rep2

source_name: Amplified total RNA from whole blood isolated 24h post-treatment from mock-treated Stat1 knockout mice

value: Stat1 KO


title: Ifnar1_Pc_rep3

source_name: Amplified total RNA from whole blood isolated 24h post-treatment from P. chabaudi-infected Ifnar1 knockout mice

value: Ifnar1 KO


title: Ifnar1 Ifngr1_Pc_rep3


title: Stat1_mock_rep1


title: Ifnar1 Ifngr1_mock_rep1


title: Ifnar1 Ifngr1_Pc_rep2


title: Ifnar1 Ifngr1_Pc_rep1


title: Ifnar1 Ifngr1_mock_rep4


title: Stat1_Pc_rep2

source_name: Amplified total RNA from whole blood isolated 24h post-treatment from P. chabaudi-infected Stat1 knockout mice


title: RPE/T/aIFNgaTNFa rep1

city: Copenhagen

first: Carsten

last: Faber

address: Blegdamsvej 3

department: Fac. of Health Science, ISIM

country: Denmark

institute: University of Copenhagen

description: SAMPLE 16

hyb_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark

data_processing: Expression Console 1.1 (Affymetrix)

label: Biotin

source_name: RPE_activated T cells_antiIFNg_antiTNFa

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

growth_protocol: The adult human RPE cell line ARPE-19 (American Type Culture Collection) was cultured in 6-well cell culture plates on Anopore 0.2 um membrane inserts (Nunc) at 37 oC with 10% CO2 >6 weeks in DMEM+10%FCS, until pigmented monolayers had formed. Then media was gradually changed to X-vivo 15 serum-free medium (Lonza BioWhittaker) prior to experiments.

extract_protocol: NucleoSpin RNA II kit (Macherey-Nagel)

treatment_protocol: ARPE19 were stimulated basolaterally for 48h with 1) recombinant IFNg (200ng/ml) and/or recombinant TNFa (40ng/ml) or 2) CD3/CD28 activated T cells (2.5 T cells/RPE cell) with anti-IFNg (40ug/ml) and/or anti-TNFa (118ug/ml).

tag: cell line

value: Retinal pigment epithelial (RPE) cells

tag: treated with

value: activated T cells and antiIFNg and antiTNFa (neutralizing antibodies)


title: Ifnar1_Pc_rep2


title: Ifnar1_Pc_rep1


title: Ifnar1 Ifngr1_mock_rep2


title: RPE/T/aIFNgaTNFa rep2

description: SAMPLE 17

scan_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark

tag: cell type


title: Ifnar1_mock_rep2

source_name: Amplified total RNA from whole blood isolated 24h post-treatment from mock-treated Ifnar1 knockout mice


title: Stat1_Pc_rep1


title: RPE/T/aTNFa rep2

description: SAMPLE 15

source_name: RPE_activated T cells_antiTNFa

value: activated T cells and antiTNFa (neutralizing antibody)


title: Ifnar1_mock_rep3


title: RPE/T/aIFNg rep1

description: SAMPLE 12

source_name: RPE_activated T cells_antiIFNg

value: activated T cells and antiIFNg (neutralizing antibody)


title: Ifngr1_Pc_rep2

source_name: Amplified total RNA from whole blood isolated 24h post-treatment from P. chabaudi-infected Ifngr1 knockout mice

value: Ifngr1 KO


title: Ifngr1_Pc_rep3


title: RPE/T/aTNFa rep1

description: SAMPLE 14


title: RPE/T rep1

description: SAMPLE 10

source_name: RPE_activated T cells

value: activated T cells


title: RPE/T rep2

description: SAMPLE 11


title: RPE/IFNgTNFa rep2

description: SAMPLE 9

value: recombinant cytokines IFNg and TNFa


title: RPE/T/aIFNg rep2

description: SAMPLE 13


title: Ifnar1_mock_rep1


title: RPE/IFNgTNFa rep1

description: SAMPLE 8


title: Ifngr1_Pc_rep1


title: B6_Pc_rep9

source_name: Amplified total RNA from whole blood isolated 24h post-treatment from P. chabaudi-infected C57BL/6 mice

value: wild type


title: Ifngr1_mock_rep3

source_name: Amplified total RNA from whole blood isolated 24h post-treatment from mock-treated Ifngr1 knockout mice


title: BalbC macrophages infected with Killed parasite (KP) at T24, rep2

city: Tunis

first: lamia

last: Guizani-Tabbane

address: 13, Place Pasteur BP74. Tunis-Belvedere

department: Immunopathology

country: Tunisia

institute: Insitut Pasteur de Tunis

description:
Kp_T24_B48
Gene expression data from BalbC macrophages infected with KP at T24

hyb_protocol: 100 ng of Total RNA were proceeded according to the GeneChip whole transcript sense target labeling assay manual using the GeneChip WT cDNA Synthesis, amplification Kit and WT terminal labeling Kit. The fragmented and labeled ssDNA was hybridized to a GeneChip Mouse Gene 1.0 ST array, washed with the Fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 30007G.

data_processing: The data preprocessing step included intrachip and interchip normalisation and summarisation. The intrachip normalisation step corrects for the GC content of the probes, the interchip normalisation step reduces non-biological differences between chips and the summarisation step combines the probe intensities into single gene expression values. For the intrachip normalisation the 'Model-based Analysis of Tiling-arrays' (MAT) was implemented as described by Kapur, Ket al., 2007. Genome Biol 8:R82, since this method  provides the most advanced GC correction for whole-transcript prepared samples. As a last step in the preprocessing of the data we applied a summarisation of probe intensities to a probe set expression [Processed/nomalized data and additional data processing details were provided as Series supplementary files].

source_name: Mouse Macrophges at 24 hrs post infection with heat killed Leishmania major parasite

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Bone Marrow cells were grown for 7 days, with re-feeding on day 3, to induce macrophage differentiation. Generated macrophages were assessed by flow cytometry for expression of F4/80 (around 90% were positive).

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

treatment_protocol: BMdM were incubated at a parasite to cell ratio of 10:1 with Ficoll purified metacyclic promastigotes of Leishmania major at 37°C in 5% CO2 during respectively T1,T3,T6,T12 and T24 hours post infection.

value: wild type BALB/c (Elevage Janvier)

value: Bone Marrow-derived macrophage (BMdM)


title: BalbC macrophages infected with Killed parasite (KP) at T24, rep1

description:
Kp_T24_B32
Gene expression data from BalbC macrophages infected with KP at T24


title: BalbC macrophages infected with Killed parasite (KP) at T12, rep3

description:
Kp_T12_B47
Gene expression data from BalbC macrophages infected with KP at T12

source_name: Mouse Macrophges at 12 hrs post infection with heat killed Leishmania major parasite


title: BalbC macrophages infected with Killed parasite (KP) at T12, rep2

description:
Kp_T12_B29
Gene expression data from BalbC macrophages infected with KP at T12


title: BalbC macrophages infected with Killed parasite (KP) at T12, rep1

description:
Kp_T12_B13
Gene expression data from BalbC macrophages infected with KP at T12


title: B6_Pc_rep8


title: B6_Pc_rep10


title: Ifngr1_mock_rep1


title: RPE/TNFa rep1

description: SAMPLE 6

value: recombinant cytokine TNFa


title: RPE/IFNg rep1

description: SAMPLE 4

value: recombinant cytokine IFNg


title: RPE/IFNg rep2

description: SAMPLE 5


title: Ifngr1_mock_rep2

value: Mock

value: whole blood


title: RPE/TNFa rep2

description: SAMPLE 7


title: RPE/- rep2

description: SAMPLE 2

source_name: RPE_alone (control)


title: BalbC macrophages infected with Killed parasite (KP) at T6, rep3

description:
Kp_T6_B46r
Gene expression data from BalbC macrophages infected with KP at T6

source_name: Mouse Macrophges at 6 hrs post infection with heat killed Leishmania major parasite


title: RPE/- rep1

description: SAMPLE 1


title: RPE/- rep3

description: SAMPLE 3


title: BalbC macrophages infected with Killed parasite (KP) at T24, rep3

description:
Kp_T24_B16r
Gene expression data from BalbC macrophages infected with KP at T24


title: BalbC macrophages infected with Killed parasite (KP) at T6, rep2

description:
Kp_T6_B26r
Gene expression data from BalbC macrophages infected with KP at T6


title: BalbC macrophages infected with Killed parasite (KP) at T6, rep1

description:
Kp_T6_B10
Gene expression data from BalbC macrophages infected with KP at T6


title: BalbC macrophages infected with Killed parasite (KP) at T3, rep3

description:
Kp_T3_B45r
Gene expression data from BalbC macrophages infected with KP at T3

source_name: Mouse Macrophges at 3 hrs post infection with heat killed Leishmania major parasite


title: Olive_cultivar Kalamon_45days of post-stress_control replicate 3

description: KA_c_45ps rep3

source_name: Olive cv. Kalamon roots 45days post-stress_control

value: Kalamon (salt-tolerant)

value: root


title: BalbC macrophages infected with Killed parasite (KP) at T1, rep2

description:
Kp_T1_B44
Gene expression data from BalbC macrophages infected with KP at T1

source_name: Mouse Macrophges at 1 hr post infection with heat killed Leishmania major parasite


title: BalbC macrophages infected with Killed parasite (KP) at T1, rep1

description:
Kp_T1_B4
Gene expression data from BalbC macrophages infected with KP at T1


title: BalbC macrophages infected with live parasite (P) at T24, rep2

description:
P_T24_B31r
Gene expression data from BalbC macrophages infected with P at T24

source_name: Mouse Macrophges at 24 hrs post infection with Leishmania major parasite


title: BalbC macrophages infected with Killed parasite (KP) at T3, rep2

description:
Kp_T3_B7r
Gene expression data from BalbC macrophages infected with KP at T3


title: BalbC macrophages infected with live parasite (P) at T24, rep3

description:
P_T24_B15r
Gene expression data from BalbC macrophages infected with P at T24


title: BalbC macrophages infected with live parasite (P) at T24, rep1

description:
P_T24_B43
Gene expression data from BalbC macrophages infected with P at T24


title: BalbC macrophages infected with Killed parasite (KP) at T1, rep3

description:
Kp_T1_B20r
Gene expression data from BalbC macrophages infected with KP at T1


title: BalbC macrophages infected with live parasite (P) at T12, rep3

description:
P_T12_B12r
Gene expression data from BalbC macrophages infected with P at T12

source_name: Mouse Macrophges at 12 hrs post infection with Leishmania major parasite


title: BalbC macrophages infected with Killed parasite (KP) at T3, rep1

description:
Kp_T3_B23
Gene expression data from BalbC macrophages infected with KP at T3


title: BalbC macrophages infected with live parasite (P) at T12, rep2

description:
P_T12_B42r
Gene expression data from BalbC macrophages infected with P at T12


title: BalbC macrophages infected with live parasite (P) at T12, rep1

description:
P_T12_B28
Gene expression data from BalbC macrophages infected with P at T12


title: BalbC macrophages infected with live parasite (P) at T6, rep2

description:
P_T6_B25
Gene expression data from BalbC macrophages infected with P at T6

source_name: Mouse Macrophges at 6 hrs post infection with Leishmania major parasite


title: BalbC macrophages infected with live parasite (P) at T6, rep3

description:
P_T6_B41r
Gene expression data from BalbC macrophages infected with P at T6


title: BalbC macrophages infected with live parasite (P) at T6, rep1

description:
P_T6_B9
Gene expression data from BalbC macrophages infected with P at T6


title: BalbC macrophages infected with live parasite (P) at T3, rep3

description:
P_T3_B6r
Gene expression data from BalbC macrophages infected with P at T3

source_name: Mouse Macrophges at 3 hrs post infection with Leishmania major parasite


title: B6_Pc_rep2

source_name: pooled reference amplified RNA from combination of universal mouse reference and samples

value: P. chabaudi


title: BalbC macrophages infected with live parasite (P) at T3, rep2

description:
P_T3_B40
Gene expression data from BalbC macrophages infected with P at T3


title: B6_Pc_rep1

value: pooled reference amplified RNA from combination of universal mouse reference and samples


title: B6_Pc_rep3


title: B6_Pc_rep4


title: B6_Pc_rep7


title: B6_mock_rep7

source_name: Amplified total RNA from whole blood isolated 24h post-treatment from mock-treated C57BL/6 mice


title: B6_mock_rep3


title: B6_mock_rep4


title: B6_Pc_rep5


title: BalbC macrophages infected with live parasite (P) at T3, rep1

description:
P_T3_B22r
Gene expression data from BalbC macrophages infected with P at T3


title: B6_Pc_rep6


title: BalbC macrophages infected with live parasite (P) at T1, rep3

description:
P_T1_B3r
Gene expression data from BalbC macrophages infected with P at T1

source_name: Mouse Macrophges at 1 hr post infection with Leishmania major parasite


title: voz1_voz2_14d_seedlings_rep1

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

description:
voz1_voz2_rep1
Gene expression of 14d whole seedlings of voz1 voz2 double mutant.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE hybridization buffer HI-PRM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis 3 Oligo Microarray (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel was set to Green, extended Dynamic range was selected and Green PMT was set to 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. All signal values were divided by the median value of all filter-passed spots.

organism: Arabidopsis thaliana

source_name: voz1 voz2 14d seedlings

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.8 ug RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown on half-strength MS agar medium in a 16h-light / 8h-dark cycle at 22°C for 14 days.

extract_protocol: Total RNA was extracted by the Plant RNeasy kit (Qiagen).

treatment_protocol: No treatment.

value: whole seedlings

tag: age

value: 14 days

value: voz1 voz2


title: B6_mock_rep1


title: BalbC macrophages infected with live parasite (P) at T1, rep2

description:
P_T1_B39
Gene expression data from BalbC macrophages infected with P at T1


title: BalbC macrophages infected with live parasite (P) at T1, rep1

description:
P_T1_B19
Gene expression data from BalbC macrophages infected with P at T1


title: voz1_voz2_14d_seedlings_rep2

description:
voz1_voz2_rep2
Gene expression of 14d whole seedlings of voz1 voz2 double mutant.


title: Non Infected BalbC macrophages at T24, rep2

description:
NI_T24_B38r
Gene expression data from non infected (NI) BalbC macrophages at T24

source_name: Non infected (NI) Mouse Macrophges at 24 hrs


title: Non Infected BalbC macrophages at T24, rep3

description:
NI_T24_B30r
Gene expression data from non infected (NI) BalbC macrophages at T24


title: 35S:AtIBH1-SRDX Arabidopsis rep3

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).
Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes.

source_name: 35S:AtIBH1-SRDX 10d whole seedlings

label_protocol: 1 µg of total RNA was used for labeling procedure using QickAmp Labeling kit (Two-color) (Agilent).

growth_protocol: All plants were grown in MS (1% sucrose) agar media in 16hr light / 8hr dark cycle in 23 Celsius degree.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

value: seedling

source_name: Wild-type 10d whole seedlings

value: wt


title: B6_mock_rep5


title: B6_mock_rep2


title: B6_mock_rep10


title: B6_mock_rep9


title: 35S:AtIBH1-SRDX Arabidopsis rep1


title: B6_mock_rep8


title: Non Infected BalbC macrophages at T24, rep1

description:
NI_T24_B14
Gene expression data from non infected (NI) BalbC macrophages at T24


title: B6_mock_rep6


title: Non Infected BalbC macrophages at T12, rep3

description:
NI_T12_B37
Gene expression data from non infected (NI) BalbC macrophages at T12

source_name: Non infected (NI) Mouse Macrophges at 12 hrs


title: Non Infected BalbC macrophages at T6, rep3

description:
NI_T6_B24r
Gene expression data from non infected (NI) BalbC macrophages at T6

source_name: Non infected (NI) Mouse Macrophges at 6 hrs


title: Non Infected BalbC macrophages at T12, rep1

description:
NI_T12_B11
Gene expression data from non infected (NI) BalbC macrophages at T12


title: Non Infected BalbC macrophages at T12, rep2

description:
NI_T12_B27r
Gene expression data from non infected (NI) BalbC macrophages at T12


title: Non Infected BalbC macrophages at T6, rep2

description:
NI_T6_B8r
Gene expression data from non infected (NI) BalbC macrophages at T6


title: Non Infected BalbC macrophages at T3, rep3

description:
NI_T3_B21r
Gene expression data from non infected (NI) BalbC macrophages at T3

source_name: Non infected (NI) Mouse Macrophges at 3 hrs


title: Non Infected BalbC macrophages at T6, rep1

description:
NI_T6_B36
Gene expression data from non infected (NI) BalbC macrophages at T6


title: voz1_voz2_14d_seedlings_rep3

description:
voz1_voz2_rep3
Gene expression of 14d whole seedlings of voz1 voz2 double mutant.


title: voz1_voz2_14d_seedlings_rep4

description:
voz1_voz2_rep4
Gene expression of 14d whole seedlings of voz1 voz2 double mutant.


title: wt_14d_seedlings_rep4

description:
wt_rep4
Gene expression of 14d whole seedlings of wild type.

source_name: wt Col-0 14d seedlings


title: Non Infected BalbC macrophages at T3, rep1

description:
NI_T3_B5r
Gene expression data from non infected (NI) BalbC macrophages at T3


title: Non Infected BalbC macrophages at T3, rep2

description:
NI_T3_B35r
Gene expression data from non infected (NI) BalbC macrophages at T3


title: wt_14d_seedlings_rep3

description:
wt_rep3
Gene expression of 14d whole seedlings of wild type.


title: 35S:AtIBH1-SRDX Arabidopsis rep2


title: Non Infected BalbC macrophages at T1, rep1

description:
NI_T1_B34
Gene expression data from non infected (NI) BalbC macrophages at T1

source_name: Non infected (NI) Mouse Macrophges at 1 hr


title: Non Infected BalbC macrophages at T1, rep3

description:
NI_T1_B18r
Gene expression data from non infected (NI) BalbC macrophages at T1


title: Non Infected BalbC macrophages at T0, rep3

description:
NI_T0_B17r
Gene expression data from non infected (NI) BalbC macrophages at T0

source_name: Non infected (NI) Mouse Macrophges at 0 hr


title: Old rep3

city: Los Angeles

first: John

last: Tower

state: California

address: 1020 Childs Way, RRI213

department: Biological Sciences

institute: University of Southern California

description:
Gene expression data  Old
Old 5

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

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

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

organism: Drosophila melanogaster

source_name: Old

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

growth_protocol: Standard food at 25 degrees

treatment_protocol: Young Control flies were 10 days old, old flies ("Old") were 61 days old (≈50% survival of the cohort). Hyperoxia-treated flies ("O2") were 3-day-old flies subjected to 100% oxygen atmosphere for 5 days (≈50% survival of the cohort).  For stress-treated flies and Stress Controls, vials containing 1% sucrose were prepared by adding 1.5 ml of 1% sucrose in deionized water to a Drosophila vial containing a single folded Kimwipe (Kimberly-Clark). For each stress treatment and the sugar-treated controls ("Sugar"), replicate vials of 25 flies each were subjected to the treatment, and then the flies from each vial were separately processed for RNA, and each sample was used to generate probe for one GeneChip hybridization, such that each treatment is represented by at least three biological replicates. For ionizing radiation treatment flies in standard food vials were irradiated with 5666Rads/hour for 16 hours using a Cesium source (Grammacell 40-Cesium 137, Atomic Energy, Canada) at the USC Norris Cancer Center facility, and then transferred to 1% sucrose vials for two days followed by processing for RNA. Because ionizing radiation is inhibitory to transcription, the two-day recovery period was included to allow the gene expression response to develop; recovery in sucrose vials was employed because the newly-irradiated flies have greatly reduced mobility and will adhere to the surface of a regular food vial.  For hydrogen peroxide treatment flies were placed in sucrose vials adjusted to 3% hydrogen peroxide for two days, and then processed for RNA.  For heat stress treatment flies were placed in sucrose vials at 37oC for 5.5 hours and then processed for RNA.  Controls for the effects of sucrose vials ("sugar-treated controls") were generated by placing flies in sucrose vials for two days prior to processing for RNA.

tag: strain background

value: a cross between Oregon-R wildtype and transgenic strain w[1118];P{w+ rtTA}(3)[E2]/ TM3

tag: gender

value: male

value: 61 days adult


title: Hyperoxia rep5

description:
Gene expression data  Hyperoxia
O2 5

source_name: Hyperoxia

value: 8 days adult


title: Non Infected BalbC macrophages at T1, rep2

description:
NI_T1_B2r
Gene expression data from non infected (NI) BalbC macrophages at T1

value: wild type BALB/c (Elevage Janvier)

value: Bone Marrow-derived macrophage (BMdM)


title: Old rep2

description:
Gene expression data  Old
Old 3


title: Hyperoxia rep6

description:
Gene expression data  Hyperoxia
O2 6


title: Non Infected BalbC macrophages at T0, rep1

description:
NI_T0_B1r
Gene expression data from non infected (NI) BalbC macrophages at T0


title: wt_14d_seedlings_rep1

description:
wt_rep1
Gene expression of 14d whole seedlings of wild type.


title: Old rep1

description:
Gene expression data  Old
Old 2


title: wt_14d_seedlings_rep2

description:
wt_rep2
Gene expression of 14d whole seedlings of wild type.


title: Hyperoxia rep4

description:
Gene expression data  Hyperoxia
O2 4


title: Young controls rep6

description:
Gene expression data  Young controls
YoungControl 6

source_name: Young controls

value: 10 days adult


title: Hyperoxia rep2

description:
Gene expression data  Hyperoxia
O2 2


title: Hyperoxia rep3

description:
Gene expression data  Hyperoxia
O2 3


title: Breast cancer cell line, SKBR3_Single_cell_2 (244k)

type: genomic

city: Oslo

first: Randi

last: Mathiesen

address: Montebello

department: Dept. of genetics

country: Norway

institute: Institute for cancer research Oslo University Hospital Radiumhospitalet

description:
SKBR3_Single_cell_2
Breast cancer cell line.

hyb_protocol: Cot-1 DNA, Agilent blocking agent and Hybridization buffer were added to the Cy3 and Cy5 labeled gDNA mix. Hybridization to microarray rotating in a hybridization oven at 65ºC for 40 hrs (244K) or 20 hrs (44K). Washing of microarrays with Agilent wash buffer 1 and 2, and NO acetonitrile or Agilent Stabilization and Drying Solution.

scan_protocol: Images were scanned with the Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction 10.5.1.1. Lowess normalization was performed.

molecule: genomic DNA

source_name: breast cancer cell line, single cell

label_protocol: 1.25ug (244K) or 750ng (44K) of amplified DNA from single cells and reference were labeled using the Agilent DNA Labeling Kit PLUS (containing random primers, 10X dNTPs, exo-Klenow-polymerase, buffer and Cy3- and Cy5-dUTPs). Test samples were labeled with Cy5 and reference with Cy3. The standard protocol (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis v.3.0) was followed.

extract_protocol: For the single cells: All samples were amplified using the GenomePlex® Single Cell Whole Genome Amplification Kit (Sigma-Aldrich, Missouri, USA) according to the manufacturer's instructions with some modifications. Clean up was performed according to the manufacturer's instructions with the Gen elute™ PCR clean up kit (Sigma-Aldrich, Missouri, USA). DNA concentrations were measured using the NanoDrop® ND-1000 (Thermo Fisher Scientific, Delaware, USA). For the 3 primary tumors: Primary tumor DNA was extracted using an ABI 341 Nucleic Acid Purification System (Applied Biosystems, Carlsbad, CA, USA) according to the manufacturer's protocol.

value: breast cancer

source_name: DNA from SKBR3

value: reference

tag: vendor; catalog#

value: LGC Standards (Middlesex, United Kingdom)


title: Old rep4

description:
Gene expression data  Old
Old 6


title: Non Infected BalbC macrophages at T0, rep2

description:
NI_T0_B33
Gene expression data from non infected (NI) BalbC macrophages at T0


title: Breast cancer, Mm4355_17_Q59_27 (44k)

description:
Mm4355_17_Q59_27
Metastatic breast cancer patient.

source_name: peripheral blood, circulating tumor cell (CTC)

value: peripheral blood

tag: type of isolated tumor cells

value: circulating tumor cell (CTC)

tag: disease state

value: metastatic breast cancer

tag: patient identifier

source_name: Human reference DNA

value: female

tag: donor

value: multiple anonymous donors

value: Promega (Madison, WI, USA); cat.# G1521


title: Breast cancer cell line, SKBR3_pool_of_single_cells (244k)

description:
SKBR3_pool_of_single_cells
Breast cancer cell line.

source_name: breast cancer cell line, pool of single cells


title: Young controls rep5

description:
Gene expression data  Young controls
YoungControl 5

tag: genotype/variation


title: Breast cancer cell line, SKBR3_Single_cell_3 (244k)

description:
SKBR3_Single_cell_3
Breast cancer cell line.


title: Hyperoxia rep1

description:
Gene expression data  Hyperoxia
O2 1


title: Breast cancer cell line, SKBR3_Single_cell_1 (244k)

description:
SKBR3_Single_cell_1
Breast cancer cell line.


title: Breast cancer, Mm4355_17_M40-3_02 (44k)

description:
Mm4355_17_M40-3_02
Metastatic breast cancer patient.

tag: tissue


title: Breast cancer, MicMa107_PT_180608 (244k)

description:
MicMa107_PT_180608
Early stage breast cancer patient.

source_name: fresh-frozen breast cancer tumor

value: breast cancer tumor

value: early-stage breast cancer

tag: sample type


title: Breast cancer, Mm4355_04_K36-3_07 (44k)

description:
Mm4355_04_K36-3_07
Metastatic breast cancer patient.


title: Normal cell from healthy donor, NBM031_25_09 (244k)

description:
NBM031_25_09
Healthy donor.

source_name: bone-marrow aspiration, normal hematopoietic cell (HC)

value: bone marrow

value: normal hematopoietic cell (HC)

value: healthy


title: Young controls rep3

description:
Gene expression data  Young controls
YoungControl 3

value: a cross between Oregon-R wildtype and transgenic strain w[1118];P{w+ rtTA}(3)[E2]/ TM3

value: male


title: Young controls rep4

description:
Gene expression data  Young controls
YoungControl 4

value: 10 days adult


title: Breast cancer, Mm4355_00_HH03 (44k)

description:
Mm4355_00_HH03
Metastatic breast cancer patient.


title: Breast cancer, MicMa107_21_09 (244k)

description:
MicMa107_21_09
Early stage breast cancer patient.


title: Breast cancer, Mm4355_00_HH02 (44k)

description:
Mm4355_00_HH02
Metastatic breast cancer patient.


title: Breast cancer, Mm4355_17_O60_13 (44k)

description:
Mm4355_17_O60_13
Metastatic breast cancer patient.


title: Breast cancer, MicMa107_21_N39-2_12 (244k)

description:
MicMa107_21_N39-2_12
Early stage breast cancer patient.

source_name: bone-marrow aspiration, disseminated tumor cell (DTC)

value: disseminated tumor cell (DTC)


title: Breast cancer cell line, SKBR3_large_amount_of_cells (244k)

description:
SKBR3_large_amount_of_cells
Breast cancer cell line.

source_name: breast cancer cell line, large amount of cells

value: breast cancer

value: reference


title: Breast cancer, MicMa107_21_S39_19 (244k)

description:
MicMa107_21_S39_19
Early stage breast cancer patient.


title: Breast cancer, Mm4329_07_L50-4_05 (44k)

description:
Mm4329_07_L50-4_05
Metastatic breast cancer patient.

value: peripheral blood


title: Breast cancer, Mm4329_01_O46-2_08 (44k)

description:
Mm4329_01_O46-2_08
Metastatic breast cancer patient.

value: circulating tumor cell (CTC)


title: Breast cancer, MicMa107_21_K45-1_18 (244k)

description:
MicMa107_21_K45-1_18
Early stage breast cancer patient.

source_name: bone-marrow aspiration, normal hematopoietic cell (HC)?

value: normal hematopoietic cell (HC)?


title: Breast cancer, Mm4329_22_O29_17 (44k)

description:
Mm4329_22_O29_17
Metastatic breast cancer patient.

value: metastatic breast cancer

value: female


title: Hydrogen peroxide rep4

description:
Gene expression data  Hydrogen peroxide
H2O2 4

source_name: Hydrogen peroxide

value: 11 days adult


title: Normal cell from healthy donor, NBM031_25_L43-3_03 (244k)

description:
NBM031_25_L43-3_03
Healthy donor.

value: multiple anonymous donors

value: Promega (Madison, WI, USA); cat.# G1521


title: Breast cancer, Mm4329_01_M40-1_05 (44k)

description:
Mm4329_01_M40-1_05
Metastatic breast cancer patient.


title: Young controls rep1

description:
Gene expression data  Young controls
YoungControl 1


title: Young controls rep2

description:
Gene expression data  Young controls
YoungControl 2


title: Breast cancer, Mm4329_00_HH07 (44k)

description:
Mm4329_00_HH07
Metastatic breast cancer patient.


title: Breast cancer, Mm4319_12_O17-4_12 (44k)

description:
Mm4319_12_O17-4_12
Metastatic breast cancer patient.


title: Breast cancer, MicMa107_21_M38_13 (244k)

description:
MicMa107_21_M38_13
Early stage breast cancer patient.

value: bone marrow

value: early-stage breast cancer


title: Hydrogen peroxide rep3

description:
Gene expression data  Hydrogen peroxide
H2O2 3


title: Breast cancer, MicMa107_11_P39-3_02 (244k)

description:
MicMa107_11_P39-3_02
Early stage breast cancer patient.


title: Breast cancer, Mm4236_16_R21-3_09 (44k)

description:
Mm4236_16_R21-3_09
Metastatic breast cancer patient.


title: Breast cancer, Mm4329_00_HH06 (44k)

description:
Mm4329_00_HH06
Metastatic breast cancer patient.


title: Breast cancer, Mm4319_10_R22-2_01 (44k)

description:
Mm4319_10_R22-2_01
Metastatic breast cancer patient.


title: Hydrogen peroxide rep2

description:
Gene expression data  Hydrogen peroxide
H2O2 2


title: Breast cancer, MicMa107_11_O39-3_10 (244k)

description:
MicMa107_11_O39-3_10
Early stage breast cancer patient.


title: Hydrogen peroxide rep1

description:
Gene expression data  Hydrogen peroxide
H2O2 1


title: Breast cancer, Mm4236_16_Q16-2_11 (44k)

description:
Mm4236_16_Q16-2_11
Metastatic breast cancer patient.


title: Mesoderm progenitors versus rest of the 8-cell embryo replicate 7

city: Basel

first: Peter

last: Nestorov

address: Maulbeerstr. 66

country: Switzerland

institute: FMI

description: biological replicate 2 of 2; technical replicate 5 of 6

hyb_protocol: Microarray hybridization was performed described in Agilent’s protocol “Two-colour microarray-based gene expression analysis”, v. 5.5 (2007). Washing was performed with stabilization and drying solution as described in the supplemental procedures of the same protocol.

scan_protocol: Scanned on a GenePix 4000B scanner (Axon); Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing:
Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization.
The datasets were analyzed as described in the Methods part of the manuscript.

organism: Parhyale hawaiensis

source_name: ectoderm, endoderm and germline progenitor blastomeres

label_protocol: Low Input RNA Amplification Kit Plus (Agilent)

extract_protocol: Trizol reagent and Qiagen Rneasy Micro Kit following manufacturer's instructions

tag: developmental stage

source_name: mesoderm progenitor blastomeres

value: mesoderm progenitor blastomeres


title: Breast cancer, Mm4236_16_L39-1_02 (44k)

description:
Mm4236_16_L39-1_02
Metastatic breast cancer patient.


title: Breast cancer, Mm4236_08_J38_10 (44k)

description:
Mm4236_08_J38_10
Metastatic breast cancer patient.


title: Sugar rep3

description:
Gene expression data  Sugar
Sugar 3

source_name: Sugar

value: a cross between Oregon-R wildtype and transgenic strain w[1118];P{w+ rtTA}(3)[E2]/ TM3


title: Sugar rep2

description:
Gene expression data  Sugar
Sugar 2

value: male


title: Sugar rep4

description:
Gene expression data  Sugar
Sugar 4


title: Breast cancer, Mm4236_08_M45-1_12 (44k)

description:
Mm4236_08_M45-1_12
Metastatic breast cancer patient.


title: Breast cancer, MicMa107_11_N35-1_11 (244k)

description:
MicMa107_11_N35-1_11
Early stage breast cancer patient.


title: Mesoderm progenitors versus rest of the 8-cell embryo replicate 6

description: biological replicate 2 of 2; technical replicate 4 of 6

value: ectoderm, endoderm and germline progenitor blastomeres


title: Breast cancer, MicMa107_11_O37-1_06 (244k)

description:
MicMa107_11_O37-1_06
Early stage breast cancer patient.

value: disseminated tumor cell (DTC)


title: Mesoderm progenitors versus rest of the 8-cell embryo replicate 8

description: biological replicate 2 of 2; technical replicate 6 of 6


title: Breast cancer, Mm4236_08_Q39-3_12 (44k)

description:
Mm4236_08_Q39-3_12
Metastatic breast cancer patient.


title: Breast cancer, Mm4236_16_R39-2_05 (44k)

description:
Mm4236_16_R39-2_05
Metastatic breast cancer patient.


title: Breast cancer, Mm4236_08_H15-3_11 (44k)

description:
Mm4236_08_H15-3_11
Metastatic breast cancer patient.


title: Breast cancer, MicMa107_11_J41-4_04 (244k)

description:
MicMa107_11_J41-4_04
Early stage breast cancer patient.


title: Breast cancer, MicMa107_11_J36_05 (244k)

description:
MicMa107_11_J36_05
Early stage breast cancer patient.


title: Sugar rep1

description:
Gene expression data  Sugar
Sugar 1


title: Mesoderm progenitors versus rest of the 8-cell embryo replicate 3

description: biological replicate 2 of 2; technical replicate 1 of 6


title: Mesoderm progenitors versus rest of the 8-cell embryo replicate 4

description: biological replicate 2 of 2; technical replicate 2 of 6


title: Mesoderm progenitors versus rest of the 8-cell embryo replicate 5

description: biological replicate 2 of 2; technical replicate 3 of 6


title: Breast cancer, MicMa083_09_T41-2_02 (244k)

description:
MicMa083_09_T41-2_02
Early stage breast cancer patient.


title: Breast cancer, Mm4236_02_R20-2_10 (44k)

description:
Mm4236_02_R20-2_10
Metastatic breast cancer patient.


title: Ionizing radiation rep3

description:
Gene expression data  Ionizing radiation
IR 3

source_name: Ionizing radiation


title: Breast cancer, MicMa083 _PT_141108 (244k)

description:
MicMa083_PT_141108
Early stage breast cancer patient.

value: breast cancer tumor


title: Breast cancer, MicMa083_15_13 (244k)

description:
MicMa083_15_13
Early stage breast cancer patient.

value: normal hematopoietic cell (HC)

value: reference


title: Mesoderm progenitors versus rest of the 8-cell embryo replicate 2

description: biological replicate 1 of 2; technical replicate 2 of 2


title: Mesoderm progenitors versus rest of the 8-cell embryo replicate 1

description: biological replicate 1 of 2; technical replicate 1 of 2


title: Ionizing radiation rep4

description:
Gene expression data  Ionizing radiation
IR 4


title: Breast cancer, Mm4236_02_18 (44k)

description:
Mm4236_02_18
Metastatic breast cancer patient.

value: peripheral blood

value: circulating tumor cell (CTC)


title: Ectoderm progenitors versus rest of the 8-cell embryo replicate 7

description: biological replicate 3 of 3; technical replicate 2 of 2

source_name: mesoderm, endoderm and germline progenitor blastomeres

source_name: ectoderm progenitor blastomeres

value: ectoderm progenitor blastomeres


title: Breast cancer, Mm4100_18_W38_17 (44k)

description:
Mm4100_18_W38_17
Metastatic breast cancer patient.

value: metastatic breast cancer

value: female


title: Ionizing radiation rep2

description:
Gene expression data  Ionizing radiation
IR 2

value: 11 days adult


title: Breast cancer, Mm4100_18_L14-2_23 (44k)

description:
Mm4100_18_L14-2_23
Metastatic breast cancer patient.

value: multiple anonymous donors

value: Promega (Madison, WI, USA); cat.# G1521


title: Ectoderm progenitors versus rest of the 8-cell embryo replicate 6

description: biological replicate 3 of 3; technical replicate 1 of 2

value: mesoderm, endoderm and germline progenitor blastomeres


title: Breast cancer, Mm4100_03_L20-1_05 (44k)

description:
Mm4100_03_L20-1_05
Metastatic breast cancer patient.


title: Ionizing radiation rep1

description:
Gene expression data  Ionizing radiation
IR 1


title: Breast cancer, Mm2235_24_N41_04 (44k)

description:
Mm2235_24_N41_04
Metastatic breast cancer patient.


title: Heat stress rep3

description:
Gene expression data  Heat stress
HS 3

source_name: Heat stress

value: 9 days adult


title: Breast cancer, MicMa003_PT_270608 (244k)

description:
MicMa003_PT_270608
Early stage breast cancer patient.

value: early-stage breast cancer


title: Ectoderm progenitors versus rest of the 8-cell embryo replicate 5

description: biological replicate 2 of 3; technical replicate 3 of 3


title: Breast cancer, MicMa017_31_02 (44k)

description:
MicMa017_31_02
Early stage breast cancer patient.

value: bone marrow


title: Breast cancer, MicMa003_26_03 (244k)

description:
MicMa003_26_03
Early stage breast cancer patient.


title: Breast cancer, MicMa003_26_K41_16 (244k)

description:
MicMa003_26_K41_16
Early stage breast cancer patient.


title: Breast cancer, MicMa083_09_T32-4_05 (244k)

description:
MicMa083_09_T32-4_05
Early stage breast cancer patient.


title: Breast cancer, MicMa083_09_S42-2_01 (244k)

description:
MicMa083_09_S42-2_01
Early stage breast cancer patient.


title: Heat stress rep2

description:
Gene expression data  Heat stress
HS 2

value: a cross between Oregon-R wildtype and transgenic strain w[1118];P{w+ rtTA}(3)[E2]/ TM3

value: male


title: Heat stress rep1

description:
Gene expression data  Heat stress
HS 1


title: Breast cancer, MicMa003_26_Q31-1_12 (244k)

description:
MicMa003_26_Q31-1_12
Early stage breast cancer patient.

value: disseminated tumor cell (DTC)


title: Ectoderm progenitors versus rest of the 8-cell embryo replicate 4

description: biological replicate 2 of 3; technical replicate 2 of 3


title: Ectoderm progenitors versus rest of the 8-cell embryo replicate 2

description: biological replicate 1 of 3; technical replicate 2 of 2


title: Breast cancer, MicMa017_31_Selfchosen_01 (44k)

description:
MicMa017_31_Selfchosen_01
Early stage breast cancer patient.

value: normal hematopoietic cell (HC)


title: Breast cancer, MicMa017_31_Selfchosen_03 (44k)

description:
MicMa017_31_Selfchosen_03
Early stage breast cancer patient.

value: reference


title: Ectoderm progenitors versus rest of the 8-cell embryo replicate 3

description: biological replicate 2 of 3; technical replicate 1 of 3


title: Stress controls rep3

description:
Gene expression data  Stress controls
StressControl 3

source_name: Stress controls


title: Breast cancer, MicMa107_11_P39-3_02 (44k)

description:
MicMa107_11_P39-3_02
Early stage breast cancer patient.


title: Breast cancer, MicMa009_27_16 (44k)

description:
MicMa009_27_16
Early stage breast cancer patient.


title: Breast cancer, MicMa003_26_M35-1_05 (244k)

description:
MicMa003_26_M35-1_05
Early stage breast cancer patient.


title: Early stage (1-cell to 4-cell) versus late stage (Day2 to Day5) embryos replicate 6

description: biological replicate 3 of 3; technical replicate 2 of 2

source_name: early stage embryos

value: early stage embryos

source_name: late stage embryos

value: late stage embryos


title: Normal cell from healthy donor, NBM031_25_L43-3_03 (44k)

description:
NBM031_25_L43-3_03
Healthy donor.

value: healthy

source_name: Human reference DNA


title: Breast cancer, MicMa003_26_J35-1_13 (244k)

description:
MicMa003_26_J35-1_13
Early stage breast cancer patient.


title: Breast cancer, MicMa003_26_J33_11 (244k)

description:
MicMa003_26_J33_11
Early stage breast cancer patient.


title: Breast cancer, Mm2471_00_HG06.1 (244k)

description:
Mm2471_00_HG06.1
Metastatic breast cancer patient.

value: metastatic breast cancer


title: Stress controls rep2

description:
Gene expression data  Stress controls
StressControl 2


title: Breast cancer, Mm2141_00_HG08.3 (244k)

description:
Mm2141_00_HG08.3
Metastatic breast cancer patient.

value: female


title: Early stage (1-cell to 4-cell) versus late stage (Day2 to Day5) embryos replicate 5

description: biological replicate 3 of 3; technical replicate 1 of 2


title: Stress controls rep1

description:
Gene expression data  Stress controls
StressControl 1


title: Breast cancer, MicMa107_11_J41-4_04 (44k)

description:
MicMa107_11_J41-4_04
Early stage breast cancer patient.


title: Breast cancer, Mm2141_00_HG07.5 (244k)

description:
Mm2141_00_HG07.5
Metastatic breast cancer patient.


title: Early stage (1-cell to 4-cell) versus late stage (Day2 to Day5) embryos replicate 3

description: biological replicate 2 of 3; technical replicate 1 of 2


title: Early stage (1-cell to 4-cell) versus late stage (Day2 to Day5) embryos replicate 4

description: biological replicate 2 of 3; technical replicate 2 of 2


title: Breast cancer, MicMa107_11_O37-1_06 (44k)

description:
MicMa107_11_O37-1_06
Early stage breast cancer patient.


title: Pancreas from adult WT mice, biological replicate 2

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

institute: Centre Médical Universitaire de Genève

description: Pancreatic gene expression analysis of WT mice

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: Raw data was background adjusted, normalized and summarized by Robust Multi-array Analysis (RMA) using the Affy package from Bioconductor on R language.

source_name: Whole pancreas

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

growth_protocol: Rkip1 KO and WT mice were derived from the same colony, maintained in a C57BL/6 background.

extract_protocol: Total RNA was isolated from whole pancreas using the RNAgents Total RNA Isolation System (Promega, WI, USA)

treatment_protocol: Pancreases were rapidly dissected after the sacrifice of the animals.

value: Whole pancreas

tag: genotype

value: WT

tag: background

value: 8 weeks


title: Early stage (1-cell to 4-cell) versus late stage (Day2 to Day5) embryos replicate 2

description: biological replicate 1 of 3; technical replicate 2 of 2


title: Breast cancer, Mm2471_00_HG05.4 (244k)

description:
Mm2471_00_HG05.4
Metastatic breast cancer patient.

value: multiple anonymous donors

value: Promega (Madison, WI, USA); cat.# G1521


title: Early stage (1-cell to 4-cell) versus late stage (Day2 to Day5) embryos replicate 1

description: biological replicate 1 of 3; technical replicate 1 of 2


title: Breast cancer, MicMa107_11_J36_05 (44k)

description:
MicMa107_11_J36_05
Early stage breast cancer patient.

value: early-stage breast cancer


title: Pancreas from adult Rkip-1 KO mice, biological replicate 2

description: Pancreatic gene expression analysis of Rkip-1 KO mice

value: Rkip-1 KO


title: Pancreas from adult WT mice, biological replicate 1


title: Pancreas from adult Rkip-1 KO mice, biological replicate 3


title: Pancreas from adult WT mice, biological replicate 3


title: Breast cancer, Mm2031_00_HG09.2 (244k)

description:
Mm2031_00_HG09.2
Metastatic breast cancer patient.

value: bone marrow


title: Breast cancer, Mm2002_00_R38-4_HG07 (244k)

description:
Mm2002_00_R38-4_HG07
Metastatic breast cancer patient.


title: Breast cancer, Mm2002_00_Q39_HG05 (244k)

description:
Mm2002_00_Q39_HG05
Metastatic breast cancer patient.


title: Breast cancer, Mm2141_00_HG07.4 (244k)

description:
Mm2141_00_HG07.4
Metastatic breast cancer patient.


title: Pancreas from adult Rkip-1 KO mice, biological replicate 1


title: Streptococcus agalactiae strain A909 CiaR/LiaR mutant versus wild-type unstressed rep 1

status: Public on Nov 18 2012

city: Baltimore

first: Julie

middle: C

last: Dunning Hotopp

state: MD

address: 20 Penn St.; HSF-II; S203B

department: Institute for Genomic Sciences

institute: Univeristy of Maryland Baltimore

description: Cy3- and Cy5-labeled probes were synthesized from total RNA. One flip-dye experiment (two hybridizations) was performed with each of two independent RNA extractions, yielding a total of four hybridizations/condition. The geometric mean ratio was calculated for all good spots across all four hybridizations.

hyb_protocol: Probe pairs were resuspended in 5X SSC, 50% formamide, 0.1% SDS, 0.1 mM DTT, and 0.35 mg/mL salmon sperm DNA and hybridized to slides overnight at 42 oC. The hybridized slides were washed twice in 2X SSC, 0.1% SDS at 55 oC; twice in 0.1X SSC, 0.1% SDS at room temperature; twice in 0.1X SSC at room temperature; and once in MilliQ water at room temperature.

scan_protocol: Scanned using a GenePix4000B scanner (Molecular Devices).

data_processing: Ratios were normalized using iterative log mean centering with a 35K low intensity filter.

organism: Streptococcus agalactiae

source_name: Streptococcus agalactiae A909 CiaR/LiaR mutant

label_protocol: Amino-allyl-dUTP Cy3 and Cy5 labeled probes were synthesized from 2 μg of total RNA using Superscript II (Invitrogen), Superscript III (Invitrogen), or Powerscript (BD Biosciences). The reactions were purified using QIAquick PCR purification kit (Qiagen) using modified phosphate buffers. Cy3- or Cy5-dyes (GE Healthcare) were chemically coupled to the incorporated amino-allyl dUTP in carbonate buffer.

growth_protocol: Streptococcus agalactiae were grown for 16 hours at 37°C in Todd-Hewitt broth at normal pH 7.7.  The bacteria were then diluted 1:100 into fresh Todd-Hewitt broth and grown at 37°C to OD650 of approximately 0.300 for RNA extraction.

extract_protocol: RNA was isolated from Streptococcus agalactiae using the following method. Total RNA was isolated from bacteria grown in Todd-Hewitt broth to early-log phase, corresponding to OD650 approximately 0.300.  Bacteria were collected by centrifugation and resuspended in RNA Protect Reagent (Qiagen).  The bacteria were again pelleted by centrifugation and resuspended in buffer containing 25% glucose, 10 mM Tris, 1 mM EDTA (pH 8.0) with lysozyme (3 mg/ml) and mutanolysin (200 mcg/ml).  The bacteria were then incubated at room temperature for 10 minutes to weaken the cell wall and facilitate bacterial lysis. Bacteria were collected by centrifugation, resuspended in RNA lysis buffer (Qiagen) and lysed by centrifugation through a QiaShredder spin column. RNA was then purified using the RNeasy kit (Qiagen). Contaminating DNA was removed by on-column DNAse digestion using RNAse-free DNAse (Qiagen). The concentration of the final RNA preparation was determined using a NanoDrop ND-1000 spectrophotometer (NanDrop Technologies) before the addition of RNase inhibitor (Invitrogen).  Aliquots of the final RNA preparation were stored at -80˚C.

treatment_protocol: No specific treatments were applied to the bacteria.  Streptococcus agalactiae were grown in rich media (Todd-Hewitt broth) at normal pH 7.7 prior to RNA extraction.

tag: Streptococcus agalactiae A909deltaCiaRdeltaLiaR A909 strain from which both CiaR gene SAK_1080 and LiaR gene SAK_0392 have been deleted

source_name: Streptococcus agalactiae A909 wild-type

tag: Streptococcus agalactiae A909 wild-type


title: Streptococcus agalactiae strain A909 wild-type versus CiaR mutant unstressed rep 2

data_processing: Ratios were normalized using iterative log mean centering with a 50K low intensity filter.

organism: Streptococcus agalactiae A909

source_name: Streptococcus agalactiae A909 ciaR mutant

tag: Streptococcus agalactiae A909deltaCiaR (A909 strain from which CiaR gene SAK_1080) has been deleted


title: Streptococcus agalactiae strain A909 LiaR mutant versus wild-type unstressed rep 2

data_processing: Ratios were normalized using iterative log mean centering with a 30K low intensity filter.

source_name: Streptococcus agalactiae A909 LiaR mutant

tag: Streptococcus agalactiae A909deltaLiaR (A909 strain from which LiaR gene SAK_0392) has been deleted


title: Streptococcus agalactiae strain A909 wild-type versus CiaR/LiaR mutant unstressed rep 1


title: Streptococcus agalactiae strain A909 wild-type versus LiaR mutant unstressed rep 1


title: Streptococcus agalactiae strain A909 CiaR/LiaR mutant versus wild-type unstressed rep 2


title: Streptococcus agalactiae strain A909 wild-type versus LiaR mutant unstressed rep 2


title: Streptococcus agalactiae strain A909 wild-type versus CiaR/LiaR mutant unstressed rep 2


title: Streptococcus agalactiae strain A909 heat stress 37C v 42C rep 1

description: Cy3- and Cy5-labeled probes were synthesized from total RNA. Total of 3 hybridizations/condition. The geometric mean ratio was calculated for all good spots across all three hybridizations.

data_processing: Ratios were normalized using iterative log mean centering with a 10K low intensity filter.

growth_protocol: Streptococcus agalactiae were grown for 16 hours at 37°C in Todd-Hewitt broth at normal pH 7.7.  The bacteria were then diluted 1:100 into fresh Todd-Hewitt broth and grown at 37°C to OD650 of approximately 0.300.  Bacteria then split into two aliquots. One aliquot of bacteria then grown at 37°C for another 30 minutes prior to RNA extraction.  One aliquot of bacteria then grown at 42°C for 30 minutes prior to RNA extraction.

extract_protocol: Total RNA was isolated from Streptococcus agalactiae using the following method. Bacteria were grown in Todd-Hewitt broth to early-log phase, corresponding to OD650 approximately 0.300.  Bacteria then split into two aliquots. One aliquot of bacteria grown at 37°C for another 30 minutes prior to RNA extraction.  One aliquot of bacteria grown at 42°C for 30 minutes prior to RNA extraction.  Total RNA isolation was then performed from both samples in parallel.  Bacteria were collected by centrifugation and resuspended in RNA Protect Reagent (Qiagen).  The bacteria were again pelleted by centrifugation and resuspended in buffer containing 25% glucose, 10 mM Tris, 1 mM EDTA (pH 8.0) with lysozyme (3 mg/ml) and mutanolysin (200 mcg/ml).  The bacteria were then incubated at room temperature for 10 minutes to weaken the cell wall and facilitate bacterial lysis. Bacteria were collected by centrifugation, resuspended in RNA lysis buffer (Qiagen) and lysed by centrifugation through a QiaShredder spin column. RNA was then purified using the RNeasy kit (Qiagen). Contaminating DNA was removed by on-column DNAse digestion using RNAse-free DNAse (Qiagen). The concentration of the final RNA preparation was determined using a NanoDrop ND-1000 spectrophotometer (NanDrop Technologies) before the addition of RNase inhibitor (Invitrogen).  Aliquots of the final RNA preparation were stored at -80˚C.

treatment_protocol: Streptococcus agalactiae were grown in rich media (Todd-Hewitt broth) at normal pH 7.7, at 37°C to early log phase growth. One aliquot of bacteria were then grown at 37°C for another 30 minutes prior to RNA extraction.

tag: Streptococcus agalactiae strain A909

source_name: Streptococcus agalactiae A909 37C early log phase, exposed to 42C

treatment_protocol: Streptococcus agalactiae were grown in rich media (Todd-Hewitt broth) at normal pH 7.7, at 37°C to early log phase growth. One aliquot of bacteria were then grown at 42°C for 30 minutes prior to RNA extraction.


title: Streptococcus agalactiae strain A909 CiaR mutant versus wild-type unstressed rep 2


title: Ectoderm progenitors versus rest of the 8-cell embryo replicate 1

value: ectoderm progenitor blastomeres

value: mesoderm, endoderm and germline progenitor blastomeres


title: Breast cancer, MicMa107_11_O39-3_10 (44k)

description:
MicMa107_11_O39-3_10
Early stage breast cancer patient.

source_name: bone-marrow aspiration, disseminated tumor cell (DTC)

value: disseminated tumor cell (DTC)

tag: gender


title: 987

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

hyb_protocol: The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer's recommendations.

scan_protocol: Scanned images were subjected to visual inspection, and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression Console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

source_name: aorta, SJL/J

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

growth_protocol: 16-week-old male mice were maintained on a 12 hr light dark cycle and were fed a chow diet.

extract_protocol: Qiazol with homogenization followed by RNeasy spin columns with optional DNase per the manufacturer's protocol.

tag: strain

value: SJL/J

value: wild-type

value: aorta

value: male

tag: age

value: 16 weeks


title: 950

source_name: aorta, SWR/J

value: SWR/J


title: Stress controls rep4

description:
Gene expression data  Stress controls
StressControl 4

tag: strain background

value: a cross between Oregon-R wildtype and transgenic strain w[1118];P{w+ rtTA}(3)[E2]/ TM3

value: 9 days adult


title: Streptococcus agalactiae strain A909 CiaR mutant versus wild-type unstressed rep 1


title: Streptococcus agalactiae strain A909 wild-type versus CiaR mutant unstressed rep 1

tag: Streptococcus agalactiae wild-type


title: 970

source_name: aorta, NZW/LacJ

value: NZW/LacJ


title: 1019

source_name: aorta, RIIIS/J

value: RIIIS/J


title: 1152

source_name: aorta, SEA/GnJ

value: SEA/GnJ


title: Breast cancer, MicMa107_11_N35-1_11 (44k)

description:
MicMa107_11_N35-1_11
Early stage breast cancer patient.

tag: type of isolated tumor cells

tag: disease state

value: early-stage breast cancer

tag: patient identifier

value: female

tag: donor

value: multiple anonymous donors

value: reference

tag: vendor; catalog#

value: Promega (Madison, WI, USA); cat.# G1521


title: 973

source_name: aorta, SM/J

value: SM/J

tag: genotype

tag: tissue


title: 972


title: 1117

source_name: aorta, MA/MyJ

value: MA/MyJ


title: 1018

value: wild-type


title: 1153

value: aorta


title: 1165

source_name: aorta, NON/ShiLtJ

value: NON/ShiLtJ

value: male


title: 943

source_name: aorta, NOD/ShiLtJ

value: NOD/ShiLtJ

value: 16 weeks


title: 999

source_name: aorta, LG/J

value: LG/J


title: 944


title: 1000


title: Streptococcus agalactiae strain A909 LiaR mutant versus wild-type unstressed rep 1


title: 971

value: NZW/LacJ


title: 933

source_name: aorta, PL/J

value: PL/J


title: 967

source_name: aorta, LP/J

value: LP/J


title: 966


title: Breast cancer, Mm2031_00_HG10.3 (244k)

description:
Mm2031_00_HG10.3
Metastatic breast cancer patient.

value: bone marrow

value: disseminated tumor cell (DTC)

value: metastatic breast cancer

source_name: Human reference DNA

tag: sample type


title: 1017

source_name: aorta, I/LnJ

value: I/LnJ


title: 988

source_name: aorta, KK/HlJ

value: KK/HlJ


title: 931

source_name: aorta, DBA/2J


title: 930

source_name: aorta, FVB/NJ

value: FVB/NJ


title: 934


title: 1096

source_name: aorta, CE/J

value: CE/J


title: 1097

value: wild-type


title: 929

value: aorta


title: 951

source_name: aorta, SWR/J

value: SWR/J


title: 932

value: male


title: 986

source_name: aorta, SJL/J

value: SJL/J


title: 1116

value: MA/MyJ

value: 16 weeks


title: 1166

value: NON/ShiLtJ


title: 989


title: 942

source_name: aorta, CBA/J

value: CBA/J


title: 1028

source_name: aorta, BXH9/TyJ


title: 1127

source_name: aorta, C58/J


title: 1029

source_name: aorta, BXH7/TyJ


title: 939

source_name: aorta, C3H/HeJ


title: 927

source_name: aorta, C57BL/6J


title: 1138

source_name: aorta, C57L/J


title: 1144

source_name: aorta, BXH4/TyJ


title: 1125

source_name: aorta, BXH22/KccJ


title: 1137


title: 1128


title: 974


title: 928


title: 975


title: 1074

source_name: aorta, BXH6/TyJ


title: 1115


title: 1030


title: 1027


title: 941


title: 1067

source_name: aorta, BXH8/TyJ


title: 1068


title: 940


title: 1145


title: 1126


title: 1032

source_name: aorta, BXH20/KccJ


title: 1073


title: 1103

source_name: aorta, BXH2/TyJ


title: 1104


title: 1121

source_name: aorta, BXH19/TyJ


title: 1031