title: LMP1 TES2 and IkBa super-repressor 24 hr_rep_C

city: Boston

first: Benjamin

last: Gewurz

address: 181 Longwood Ave

department: Medicine, Infectious Disease

institute: Brigham and Women's Hospital

hyb_protocol: Following Affymetrix's mannual

scan_protocol: Following Affymetrix's mannual

data_processing: Following Affymetrix's mannual

source_name: 24 hr_LMP1 TES2 and IkBa super-repressor expression

label_protocol: Following Affymetrix's mannual

growth_protocol: EBNA3CHT LCLs were grown in the presence (permissive) or the absence (non-permissive) of HT for 7 days, or transcomplemented with an OriP base EBNA3C expression vector and grown in the absence of HT for 12 weeks.

extract_protocol: Total cellular RNA was prepared using RNABee following manufacturer's mannual.

treatment_protocol: EBNA3CHT LCLs were washed with fresh RPMI media 3 times, incubated at 37C for 30 minutes and washed twice again. The cells were seeded in the HT+ or HT- media and grown for 7 days. The cell concentration was kept around 300,000/ml. EBNA3CHT LCLs were transfected with Ori-P based EBNA 3C expression plasmid and grown in HT- media for 12 weeks.

tag: background cell line

value: HEK-293 cells with inducible LMP1 TES2  and IkBa super-repressor

tag: growth condition

value: 24 hours doxycyline/4HT


title: LMP1 TES2 and IkBa super-repressor 12 hr_rep_C

status: Public on May 15 2011

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 12 hr_LMP1 TES2 and IkBa super-repressor expression

tag: cell type

value: 12 hours doxycyline/4HT


title: LMP1 TES2 and IkBa super-repressor 12 hr_rep_B


title: LMP1 TES2 and IkBa super-repressor 24 hr_rep_B


title: LMP1 TES2 and IkBa super-repressor 24 hr_rep_A


title: LMP1 TES2 and IkBa super-repressor 12 hr_rep_A


title: ACPS_3

status: Public on May 16 2011

city: Cambridge

first: Dean

last: Baker

address: Department of Genetics, Downing Street

country: United Kingdom

institute: University of Cambridge

description: Anopheles male Acps

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Plasmodium/Anopheles Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 7G.

data_processing: The data were analyzed with [R] Bioconductor using the GC-RMA normalization and MAS probe detection libraries.

organism: Anopheles gambiae

source_name: Anopheles male Acps

label_protocol: Biotinylated cRNA was prepared according to the standard two-cycle Affymetrix protocol from 50ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: 5 day old male and female mosquitoes.  Samples for males and females where blooded after the bloodmeal over at three time points over 72hrs (24hrs, 48hr, 72hrs)

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen)

treatment_protocol: Mosquitoes were anaesthetised briefly by chilling on ice, then immediately dissected.

tag: stage

value: adult

tag: tissue

value: acps

tag: gender

value: male


title: LMP1 TES2 and IkBa super-repressor 9 hr_rep_C

source_name: 9 hr_LMP1 TES2 and IkBa super-repressor expression

value: 9 hours doxycyline/4HT


title: E.coli cells at 3.5 hrs after addition of high IPTG (1.0 mM), biological rep2, technical rep2

city: Newark

first: Kelvin

middle: H.

last: Lee

state: DE

address: 15 Innovation Way

department: Biotechnology Institute

institute: University of Delaware

description: Gene expression data from E.coli cells at 3.5hrs after induction with 1.0 mM IPTG

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix's GeneChip E. coli Antisense Genome Array [Ecoli_ASv2]. GeneChips were washed and stained in the GeneChip® Fluidics Station 450.

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

data_processing: The probe intensity data  was analyzed using Genetraffic software (Iobion Informatics LLC, La Jolla, CA, USA). The probe intensity data was normalized using GC-RMA algorithm.

organism: Escherichia coli

source_name: E.coli cells at 3.5 hrs after induction with 1.0 mM IPTG

label_protocol: cRNA was labeled using the NuGEN’s Ovation™ Biotin RNA Amplification and Labeling System.

extract_protocol: Total RNA was extracted using MasterPure RNA purification kits (Epicentre, Madison, WI, USA) according to the manufacturer’s protocol

treatment_protocol: Cells corresponding to 10 ml culture volume were harvested at 3.5 hrs after induction with 1.0 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater.


title: E.coli cells at 3.5 hrs after addition of low IPTG (0.1 mM), biological rep1, technical rep2

description: Gene expression data from E.coli cells at 3.5hrs after induction with 0.1 mM IPTG

source_name: E.coli cells at 3.5 hrs after induction with 0.1 mM IPTG

treatment_protocol: Cells corresponding to 10 ml culture volume were harvested at 3.5 hrs after induction with 0.1 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater.


title: E.coli cells at 3.5 hrs after addition of low IPTG (0.1 mM), biological rep2, technical rep2

tag: E.coli cells at 3.5 hrs after induction with 0.1 mM IPTG


title: E.coli cells at 3.5 hrs after addition of no IPTG (0 mM), biological rep1, technical rep2

description: Gene expression data from E.coli cells at 3.5hrs after induction with 0mM IPTG

source_name: E.coli cells at 3.5 hrs after induction with 0 mM IPTG

treatment_protocol: Cells corresponding to 10 ml culture volume were harvested at 3.5 hrs after induction with 0 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater.


title: E.coli cells at 3.5 hrs after addition of no IPTG (0 mM), biological rep2, technical rep2

tag: E.coli cells at 3.5 hrs after induction with 0 mM IPTG


title: E.coli cells at 1.5 hrs after addition of low IPTG (0.1 mM), biological rep1, technical rep2

description: Gene expression data from E.coli cells at 1.5hrs after induction with 0.1 mM IPTG

source_name: E.coli cells at 1.5 hrs after induction with 0.1 mM IPTG

treatment_protocol: Cells corresponding to 10 ml culture volume were harvested at 1.5 hrs after induction with 0.1 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater.


title: E.coli cells at 3.5 hrs after addition of high IPTG (1.0 mM), biological rep1, technical rep2

tag: E.coli cells at 3.5 hrs after induction with 1.0 mM IPTG


title: E.coli cells at 1.5 hrs after addition of high IPTG (1.0 mM), biological rep2, technical rep2

description: Gene expression data from E.coli cells at 1.5hrs after induction with 1.0 mM IPTG

source_name: E.coli cells at 1.5 hrs after induction with 1.0 mM IPTG

treatment_protocol: Cells corresponding to 10 ml culture volume were harvested at 1.5 hrs after induction with 1.0 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater.


title: LMP1 TES2 and IkBa super-repressor 0 hr_rep_B

source_name: 0 hr_LMP1 TES2 and IkBa super-repressor expression

value: 0 hours doxycyline/4HT


title: LMP1 TES2 and IkBa super-repressor 6 hr_rep_B

source_name: 6 hr_LMP1 TES2 and IkBa super-repressor expression

value: 6 hours doxycyline/4HT


title: LMP1 TES2 and IkBa super-repressor 9 hr_rep_B


title: LMP1 TES2 and IkBa super-repressor 6 hr_rep_A


title: E.coli cells at 1.5 hrs after addition of no IPTG (0 mM), biological rep1, technical rep2

description: Gene expression data from E.coli cells at 1.5hrs after induction with 0mM IPTG

source_name: E.coli cells at 1.5 hrs after induction with 0 mM IPTG

treatment_protocol: Cells corresponding to 10 ml culture volume were harvested at 1.5 hrs after induction with 0 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater.


title: E.coli cells at 1.5 hrs after addition of no IPTG (0 mM), biological rep2, technical rep2

tag: E.coli cells at 1.5 hrs after induction with 0 mM IPTG


title: E.coli cells at 1.5 hrs after addition of low IPTG (0.1 mM), biological rep2, technical rep2

tag: E.coli cells at 1.5 hrs after induction with 0.1 mM IPTG


title: LMP1 TES2 and IkBa super-repressor 9 hr_rep_A


title: E.coli cells at the time of IPTG induction (T=0 hrs), biological rep2, technical rep2

description: Gene expression data from E.coli cells at the time of IPTG induction

treatment_protocol: Cells corresponding to 10 ml culture volume were harvested at 0 hrs using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater.


title: LMP1 TES2 and IkBa super-repressor 6 hr_rep_C


title: E.coli cells at 1.5 hrs after addition of high IPTG (1.0 mM), biological rep1, technical rep2

tag: E.coli cells at 1.5 hrs after induction with 1.0 mM IPTG


title: E.coli cells at 3.5 hrs after addition of high IPTG (1.0 mM), biological rep1, technical rep 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (https://www.affymetrix.com/support/downloads/manuals/expression_s3_manual.pdf).


title: E.coli cells at 1.5 hrs after addition of high IPTG (1.0 mM), biological rep2, technical rep 1


title: LMP1 TES2 and IkBa super-repressor 0 hr_rep_C


title: LMP1 TES2 and IkBa super-repressor 0 hr_rep_A


title: LMP1 TES2 Only 24 hr_rep_B

source_name: 24 hr_LMP1 TES2 expression

value: HEK-293 cells with inducible LMP1 TES2


title: E.coli cells at 3.5 hrs after addition of high IPTG (1.0 mM), biological rep2, technical rep 1


title: LMP1 TES2 Only 24 hr_rep_A


title: E.coli cells at 3.5 hrs after addition of low IPTG (0.1 mM), biological rep1, technical rep 1


title: LMP1 TES2 Only 24 hr_rep_C


title: E.coli cells at 1.5 hrs after addition of high IPTG (1.0 mM), biological rep1, technical rep 1


title: E.coli cells at 3.5 hrs after addition of low IPTG (0.1 mM), biological rep2, technical rep 1


title: E.coli cells at the time of IPTG induction (T=0 hrs), biological rep1, technical rep2


title: LMP1 TES2 Only 12 hr_rep_C

source_name: 12 hr_LMP1 TES2 expression


title: E.coli cells at 1.5 hrs after addition of low IPTG (0.1 mM), biological rep2, technical rep 1


title: E.coli cells at 3.5 hrs after addition of no IPTG (0 mM), biological rep2, technical rep 1


title: E.coli cells at 3.5 hrs after addition of no IPTG (0 mM), biological rep1, technical rep 1


title: LMP1 TES2 Only 12 hr_rep_A


title: E.coli cells at 1.5 hrs after addition of no IPTG (0 mM), biological rep2, technical rep 1


title: E.coli cells at 1.5 hrs after addition of low IPTG (0.1 mM), biological rep1, technical rep 1


title: LMP1 TES2 Only 9 hr_rep_B

source_name: 9 hr_LMP1 TES2 expression


title: LMP1 TES2 Only 9 hr_rep_A


title: E.coli cells at the time of IPTG induction (T=0 hrs), biological rep2, technical rep 1


title: LMP1 TES2 Only 9 hr_rep_C


title: E.coli cells at 1.5 hrs after addition of no IPTG (0 mM), biological rep1, technical rep 1


title: LMP1 TES2 Only 6 hr_rep_B

source_name: 6 hr_LMP1 TES2 expression


title: LMP1 TES2 Only 0 hr_rep_B

source_name: 0 hr_LMP1 TES2 expression


title: E.coli cells at the time of IPTG induction (T=0 hrs), biological rep1, technical rep 1


title: LMP1 TES2 Only 0 hr_rep_C


title: LMP1 TES2 Only 6 hr_rep_C


title: LMP1 TES2 Only 0 hr_rep_A


title: LNCaP-RNA-dht-siFoxA1 rep3 [gene expr]

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: LNCaP gene expression treated with siRNA against FoxA1 and DHT for 24h

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalization with Illumina Inc. BeadStudio version 1.5.1.3

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was extracted from 5 Mio cells on Rneasy columns (Qiagen) with on-column DNase digestion following the manufacturer's instructions. RNA quality was assessed on an Agilent 2100 BioAnalyzer .

treatment_protocol: Control (1027280) and the specific siRNA against  FOXA1 (M-010319) were purchased from Qiagen or Dharmacon. One day prior to transfection, LNCaP cells were seeded in RPMI 1640 medium. Six hours after transfection with Lipofectamine 2000 (Invitrogen), cells were washed twice with PBS and then maintained in hormone-deprived phenol-free RPMI 1640 media.  Cells were then cultured for 72 hours following transfection and then treated with DHT or vehicle for 1 hrs. = Quantile normalization with Illumina Inc. BeadStudio version 1.5.1.3

value: prostate cancer cell line (LNCaP)

tag: sirna transfection

tag: agent

value: DHT


title: wild type B cells treated with LPS for 1 day

city: St. Louis

first: Kenneth

middle: M

last: Murphy

address: 660 S. Euclid

department: Pathology and Immunology

institute: Wustl/HHMI

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: standard affymetrix protocol

organism: Mus musculus

source_name: mRNA from B cells

label_protocol: standard affymetrix protocol

growth_protocol: standard tissue culture Iscoves media plus LPS

extract_protocol: Standard affymetrix

treatment_protocol: treatment with or without LPS

value: B cell


title: wild type B cells treated with LPS for 2 days


title: LNCaP-RNA-vehicle-siFoxA1 rep3 [gene expr]

description: LNCaP gene expression treated with siRNA against FoxA1 and vehicle for 24h

value: vehicle


title: LNCaP-RNA-dht-siFoxA1 rep1 [gene expr]


title: Fed-batch sample T=22h

city: Thiverval-Grignon

first: Nicolas

last: Morin

address: Av. Lucien Bretignières

department: UMR 1319 Micalis

country: France

institute: INRA

description: Fed batch sample, harvested at ca. 22H after the initiation of the culture.

hyb_protocol: Hybridization of the samples was automatically performed within a Discovery XT System (Ventana Medical Systems Inc., Roche , Switzerland) for 10h at 42°C. Specific chemicals (e.g. 2Ml BSA, detergents) were used to limitate aspecific hybridation. Arrays are washed several times before scanning, in SSC 0.1x.

scan_protocol: Scanning was performed using a INNOSCAN 700 Microarray Scanner (INNOPSYS, France). Images were quantified using the GenePix Pro v3.0 software (Molecular Devices, USA).

data_processing: Raw transcriptomic data were filtered and normalized using the R software and the Limma package of the Bioconductor library. A preliminary filtration of the dataset was performed, using the quality flags provided by the GenePix software. Spots with a quality flag value inferior to “0” were removed from the analysis. Local background estimates were corrected using the “normexp + offset” method, using an offset value of 50. Background substracted data was further normalized using a PrintTip Loess method. Whenever possible (i.e. When the number of missing values for a given spot was inferior to 30%), missing values produced during the filtration and normalization processes were simulated using the iKNN algorithm.

organism: Yarrowia lipolytica

source_name: Total RNA from pooled samples

label_protocol: Samples were reverse transcribed and labelled using the ChipShot Direct Labelling kit (Promega, USA), according to the manufacturer's instructions. Labelled cDNAs were further purified by three sequential runs in an Autoseq-50 purification column (Amersham Biosciences, GB).

extract_protocol: Frozen samples were treated by mechanical disruption, using a bead beater (Microdismenbrator, Braun, Germany) and a tungsten bead (Ø ~ 7 mm), for 2 min at 2600 rpm. After disruption, the resulting cell powder was recovered and further processed for RNA purification using the RNEasy Midi Kit (Qiagen, The Netherlands), according to the manufacturer's instruction.

treatment_protocol: Samples have been collected from the bioreactor directly through the sampling septum. For each time point, a volume equivalent to ca. 300 mg dry cell weight was harvested, frozen in liquid nitrogen, and further stored at -80°C until extraction.

tag: sample type

value: Total RNA from pooled samples

tag: strain

source_name: Fed-batch sample T=22h

tag: treatment

value: fed-batch + nitrogen limitation

tag: time


title: Fed-batch sample T=23h

description: Fed batch sample, harvested at ca. 23H after the initiation of the culture.

source_name: Fed-batch sample T=23h


title: Fed-batch sample T=26h

description: Fed batch sample, harvested at ca. 26H after the initiation of the culture.

source_name: Fed-batch sample T=26h


title: Fed-batch sample T=25h

description: Fed batch sample, harvested at ca. 25H after the initiation of the culture.

source_name: Fed-batch sample T=25h


title: 60h_Con_1

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

hyb_protocol: Appropriate Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25 mM HEPES and 3 × SSC, resulting in a final volume of 70μl. The hybridization mixtures were boiled for 2 min at 99°C and allowed to cool at room temperature for 5 min. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 63°C. Microarrays were washed twice in 0.6 × SSC, 0.01% SDS and were kept in 0.06 × SSC until analysis.

scan_protocol: Slides were dried via centrifugation and scanned using an Axon 4000B scanner. The experimental setup followed a reference design, i.e. all samples were hybridized against the same pool made up of equal amounts of aRNA from all samples.

data_processing: TIGR Spotfinder 2.2.3 was used to extract spot intensities and subtract background (Saeed et al. 2003). The data were normalized using TIGR MIDAS 2.21 printtip-specific LOWESS followed by in-slide replicates analyses (Saeed et al. 2003).

label: cy3 (IA)

organism: Orbicella faveolata

source_name: reference

label_protocol: Total RNA of approximately 1,000 coral embryos was isolated using Qiazol lysis reagent (Qiagen) according to manufacturer's instructions. RNA quantity and integrity was assessed using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. For each sample, 1ug of total RNA was amplified using the MessageAmp II aRNA kit (Ambion). Subsequent cDNA synthesis and dye-labeling was performed using 3 ug aRNA per sample were primed with 3.5 nmol random pentadecamer for 10min at 70°C. Reverse transcription (RT) lasted for 2 hours at 42°C using a master mix containing a 3:2 ratio of aminoallyl-dUTP to TTP. Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10 uL 0.5M EDTA and 10 uL 1M NaOH for 15min at 65°C. After hydrolysis, RT reactions were cleaned using the MinElute Cleanup kit (Qiagen). Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 17uL DMSO, and the coupling reactions lasted for 2hr at room temperature in the dark. Dye-coupled cDNAs were cleaned using the MinElute Cleanup kit (Qiagen). Appropriate Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25 mM HEPES and 3 × SSC, resulting in a final volume of 70ul.

extract_protocol: Total RNA Qiazol extraction, aRNA amplification, cDNA Superscript III

tag: larvae

value: pooled referenced

label: cy3 (IB)

value: sample


title: LNCaP-RNA-dht-siFoxA1 rep2 [gene expr]

tag: cell type


title: LNCaP-RNA-vehicle-siFoxA1 rep1 [gene expr]


title: Fed-batch sample T=27h

description: Fed batch sample, harvested at ca. 32H after the initiation of the culture.

source_name: Fed-batch sample T=27h


title: LNCaP-RNA-dht-siCTRL rep3 [gene expr]

description: LNCaP gene expression treated with control siRNA and DHT for 24h

source_name: LNCaP-dht-siCTRL


title: LNCaP-RNA-vehicle-siFoxA1 rep2 [gene expr]


title: batf KO B cells treated with LPS for 2 days


title: Fed-batch sample T=17h

description: Fed batch sample, harvested at ca. 17H after the initiation of the culture.

source_name: Fed-batch sample T=17h


title: Fed-batch sample T=21h

description: Fed batch sample, harvested at ca. 21H after the initiation of the culture.

source_name: Fed-batch sample T=21h


title: Fed-batch sample T=15h

description: Fed batch sample, harvested at ca. 15H after the initiation of the culture.

source_name: Fed-batch sample T=15h


title: wild type B cells unactivated


title: batf KO B cells unacivated


title: Fed-batch sample T=14h

description: Fed batch sample, harvested at ca. 14H after the initiation of the culture.

source_name: Fed-batch sample T=14h


title: batf KO B cells treated with LPS for 1 day


title: LNCaP-RNA-dht-siCTRL rep1 [gene expr]


title: LNCaP-RNA-dht-siCTRL rep2 [gene expr]


title: Fed-batch sample T=10h

description: Fed batch sample, harvested at ca. 10H after the initiation of the culture.

source_name: Fed-batch sample T=10h


title: Fed-batch sample T=7h

description: Fed batch sample, harvested at ca. 7H after the initiation of the culture.

source_name: Fed-batch sample T=7h


title: LNCaP-RNA-vehicle-siCTRL rep3 [gene expr]

description: LNCaP gene expression treated with control siRNA and vehicle for 24h

source_name: LNCaP-vehicle-siCTRL


title: LMP1 TES2 Only 12 hr_rep_B

source_name: 12 hr_LMP1 TES2 expression

tag: background cell line

tag: growth condition


title: LMP1 TES2 Only 6 hr_rep_A

source_name: 6 hr_LMP1 TES2 expression


title: LNCaP-RNA-vehicle-siCTRL rep2 [gene expr]


title: LNCaP-RNA-vehicle-siCTRL rep1 [gene expr]


title: subject_3242_technical rep 1

status: Public on May 14 2011

city: Berkeley

first: Alan

last: Hubbard

state: CA

address: School of Public Health, Div. of Biostatistics,101 Haviland Hall, MC 7358

department: Division of Biostatistics

institute: UC Berkeley

description:
technical rep 1
Chip_Id: 1897008066
Chip_Section: 18D

hyb_protocol: Following fragmentation, 850ng of cRNA were hybridized for 16 hr at 55C on Illumina Sentrix HumanRef-8 chips. Hybridization, washing and detection were performed using Illumina's recommended protocol.

scan_protocol: Scanning was performed using a BeadArray Reader and BeadScan software (Illumina)

data_processing: Data were normalized using quatile normalization from R Affy packages.

source_name: PBMC

label_protocol: cDNA was generated from total RNA (200ng) and used as a template for the in vitro transcription of biotin-labeled cRNA using the Illumina® RNA Amplification kit (Ambion, Austin, TX) according to the manufacturer’s protocol.

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

tag: benzene

tag: age

tag: gender

tag: smoking

value: yes

tag: subject id


title: subject_3169

description:
Chip_Id: 1888849020
Chip_Section: 17G

value: Ctr

value: no


title: subject_3415

description:
Chip_Id: 1897008066
Chip_Section: 18F

value: female


title: subject_3219

description:
Chip_Id: 1897008066
Chip_Section: 18G


title: subject_3386

description:
Chip_Id: 1897008066
Chip_Section: 18E

value: male


title: subject_3414

description:
Chip_Id: 1888849020
Chip_Section: 17E


title: subject_3216_technical rep 2

description:
technical rep 2
Chip_Id: 1897008066
Chip_Section: 18H


title: subject_3385

description:
Chip_Id: 1888849020
Chip_Section: 17H


title: subject_3216_technical rep 1

description:
technical rep 1
Chip_Id: 1888849020
Chip_Section: 17C


title: subject_3436

description:
Chip_Id: 1888849020
Chip_Section: 17D


title: subject_3172

description:
Chip_Id: 1897008066
Chip_Section: 18A


title: subject_3120_technical rep 1

description:
technical rep 1
Chip_Id: 1897008066
Chip_Section: 18C


title: subject_3116_technical rep 1

description:
technical rep 1
Chip_Id: 1888849020
Chip_Section: 17B


title: subject_3330

description:
Chip_Id: 1888849020
Chip_Section: 17F


title: subject_3232_technical rep 1

description:
technical rep 1
Chip_Id: 1888849020
Chip_Section: 17A


title: subject_3433

description:
Chip_Id: 1888849009
Chip_Section: 16F


title: subject_3324

description:
Chip_Id: 1888849009
Chip_Section: 16D


title: subject_3337

description:
Chip_Id: 1897008066
Chip_Section: 18B


title: subject_3413

description:
Chip_Id: 1888849009
Chip_Section: 16H


title: subject_3227_technical rep 1

description:
technical rep 1
Chip_Id: 1888849009
Chip_Section: 16A


title: subject_3412

description:
Chip_Id: 1787466069
Chip_Section: 15D


title: subject_3213

description:
Chip_Id: 1787466069
Chip_Section: 15H


title: subject_3427

description:
Chip_Id: 1787466069
Chip_Section: 15E


title: subject_3168

description:
Chip_Id: 1888849009
Chip_Section: 16C


title: subject_3109_technical rep 1

description:
technical rep 1
Chip_Id: 1888849009
Chip_Section: 16E


title: subject_3379

description:
Chip_Id: 1787466069
Chip_Section: 15G


title: subject_3225_technical rep 1

description:
technical rep 1
Chip_Id: 1787466069
Chip_Section: 15F


title: subject_3322

description:
Chip_Id: 1787466069
Chip_Section: 15C


title: subject_3207_technical rep 2

description:
technical rep 2
Chip_Id: 1787466068
Chip_Section: 14H


title: subject_3377

description:
Chip_Id: 1787466068
Chip_Section: 14F


title: subject_3167

description:
Chip_Id: 1787466069
Chip_Section: 15B


title: subject_3410

description:
Chip_Id: 1787466068
Chip_Section: 14G


title: subject_3310

description:
Chip_Id: 1787466068
Chip_Section: 14E


title: subject_3207_technical rep 1

description:
technical rep 1
Chip_Id: 1787466067
Chip_Section: 13G


title: subject_3294

description:
Chip_Id: 1787466068
Chip_Section: 14D


title: subject_3376

description:
Chip_Id: 1787466067
Chip_Section: 13E


title: subject_3108

description:
Chip_Id: 1787466069
Chip_Section: 15A


title: subject_3409

description:
Chip_Id: 1787466067
Chip_Section: 13C


title: subject_3306

description:
Chip_Id: 1787466067
Chip_Section: 13H


title: subject_3166

description:
Chip_Id: 1787466068
Chip_Section: 14B


title: subject_3381

description:
Chip_Id: 1888849009
Chip_Section: 16G


title: subject_3164

description:
Chip_Id: 1787466067
Chip_Section: 13F


title: subject_3205_technical rep 2

description:
technical rep 2
Chip_Id: 1787466067
Chip_Section: 13B


title: subject_3210

description:
Chip_Id: 1787466068
Chip_Section: 14C


title: subject_3285

description:
Chip_Id: 1787466067
Chip_Section: 13A


title: subject_3284

description:
Chip_Id: 1787466062
Chip_Section: 12D


title: subject_3205_technical rep 1

description:
technical rep 1
Chip_Id: 1787466062
Chip_Section: 12H


title: subject_3204_technical rep 2

description:
technical rep 2
Chip_Id: 1787466062
Chip_Section: 12F


title: subject_3408

description:
Chip_Id: 1787466062
Chip_Section: 12E


title: subject_3103_technical rep 1

description:
technical rep 1
Chip_Id: 1787466068
Chip_Section: 14A


title: subject_3245

description:
Chip_Id: 1787466062
Chip_Section: 12C


title: subject_3442

description:
Chip_Id: 1787466057
Chip_Section: 11E


title: subject_3102

description:
Chip_Id: 1787466067
Chip_Section: 13D


title: subject_3374

description:
Chip_Id: 1787466057
Chip_Section: 11C


title: subject_3101_technical rep 1

description:
technical rep 1
Chip_Id: 1787466062
Chip_Section: 12A


title: subject_3214

description:
Chip_Id: 1888849009
Chip_Section: 16B


title: subject_3204_technical rep 1

description:
technical rep 1
Chip_Id: 1787466057
Chip_Section: 11G


title: subject_3244

description:
Chip_Id: 1787466057
Chip_Section: 11F


title: subject_3375

description:
Chip_Id: 1787466062
Chip_Section: 12G


title: subject_3163

description:
Chip_Id: 1787466062
Chip_Section: 12B


title: subject_3407

description:
Chip_Id: 1787466057
Chip_Section: 11D


title: subject_3162

description:
Chip_Id: 1787466057
Chip_Section: 11H


title: subject_3283

description:
Chip_Id: 1787466057
Chip_Section: 11B


title: subject_3159

description:
Chip_Id: 1787466056
Chip_Section: 10E


title: subject_3282

description:
Chip_Id: 1787466056
Chip_Section: 10G


title: subject_3203_technical rep 1

description:
technical rep 1
Chip_Id: 1787466056
Chip_Section: 10B


title: subject_3203_technical rep 2

description:
technical rep 2
Chip_Id: 1787466057
Chip_Section: 11A


title: subject_3363

description:
Chip_Id: 1787466055
Chip_Section: 9H


title: subject_3198_technical rep 1

description:
technical rep 1
Chip_Id: 1787466056
Chip_Section: 10F


title: subject_3402

description:
Chip_Id: 1787466056
Chip_Section: 10D


title: subject_3365

description:
Chip_Id: 1787466056
Chip_Section: 10A


title: subject_3242_technical rep 2

description:
technical rep 2
Chip_Id: 1787466055
Chip_Section: 9G


title: subject_3431

description:
Chip_Id: 1787466055
Chip_Section: 9B


title: subject_3232_technical rep 2

description:
technical rep 2
Chip_Id: 1787466054
Chip_Section: 8D


title: subject_3399

description:
Chip_Id: 1787466055
Chip_Section: 9D


title: subject_3395

description:
Chip_Id: 1787466053
Chip_Section: 7H


title: subject_3362

description:
Chip_Id: 1787466054
Chip_Section: 8E


title: subject_3278

description:
Chip_Id: 1787466055
Chip_Section: 9F


title: subject_3229

description:
Chip_Id: 1787466053
Chip_Section: 7F


title: subject_3193_technical rep 1

description:
technical rep 1
Chip_Id: 1787466053
Chip_Section: 7G


title: subject_3198_technical rep 2

description:
technical rep 2
Chip_Id: 1787466055
Chip_Section: 9C


title: subject_3441

description:
Chip_Id: 1787466056
Chip_Section: 10C


title: subject_3153

description:
Chip_Id: 1787466054
Chip_Section: 8B


title: subject_3193_technical rep 2

description:
technical rep 2
Chip_Id: 1787466055
Chip_Section: 9A


title: subject_3396

description:
Chip_Id: 1787466054
Chip_Section: 8F


title: subject_3423

description:
Chip_Id: 1787466054
Chip_Section: 8G


title: subject_3243

description:
Chip_Id: 1787466056
Chip_Section: 10H


title: subject_3267

description:
Chip_Id: 1787466054
Chip_Section: 8A


title: subject_3359

description:
Chip_Id: 1787466053
Chip_Section: 7E


title: subject_3157

description:
Chip_Id: 1787466055
Chip_Section: 9E


title: subject_3421

description:
Chip_Id: 1787466052
Chip_Section: 6G


title: subject_3348

description:
Chip_Id: 1787466052
Chip_Section: 6D


title: subject_3120_technical rep 2

description:
technical rep 2
Chip_Id: 1787466053
Chip_Section: 7A


title: subject_3151

description:
Chip_Id: 1787466053
Chip_Section: 7B


title: subject_3422

description:
Chip_Id: 1787466053
Chip_Section: 7C


title: subject_3393

description:
Chip_Id: 1787466048
Chip_Section: 5G


title: subject_3338

description:
Chip_Id: 1787466048
Chip_Section: 5E


title: subject_3394

description:
Chip_Id: 1787466052
Chip_Section: 6H


title: subject_3226

description:
Chip_Id: 1787466048
Chip_Section: 5A


title: subject_3197

description:
Chip_Id: 1787466054
Chip_Section: 8C


title: subject_3445

description:
Chip_Id: 1787466052
Chip_Section: 6C


title: subject_3225_technical rep 2

description:
technical rep 2
Chip_Id: 1787466047
Chip_Section: 4D


title: subject_3227_technical rep 2

description:
technical rep 2
Chip_Id: 1787466052
Chip_Section: 6E


title: subject_3194

description:
Chip_Id: 1787466053
Chip_Section: 7D


title: subject_3109_technical rep 2

description:
technical rep 2
Chip_Id: 1787466048
Chip_Section: 5B


title: subject_3130_technical rep 2

description:
technical rep 2
Chip_Id: 1787466054
Chip_Section: 8H


title: subject_3444

description:
Chip_Id: 1787466048
Chip_Section: 5H


title: subject_3420

description:
Chip_Id: 1787466048
Chip_Section: 5F


title: subject_3150

description:
Chip_Id: 1787466052
Chip_Section: 6A


title: subject_3149

description:
Chip_Id: 1787466048
Chip_Section: 5C


title: subject_3392

description:
Chip_Id: 1787466047
Chip_Section: 4F


title: subject_3187

description:
Chip_Id: 1787466048
Chip_Section: 5D


title: subject_3419

description:
Chip_Id: 1787466047
Chip_Section: 4H


title: subject_3336

description:
Chip_Id: 1787466047
Chip_Section: 4A


title: subject_3188

description:
Chip_Id: 1787466052
Chip_Section: 6B


title: subject_3398

description:
Chip_Id: 1787466047
Chip_Section: 4C


title: subject_3103_technical rep 2

description:
technical rep 2
Chip_Id: 1787466047
Chip_Section: 4G


title: subject_3186

description:
Chip_Id: 1787466047
Chip_Section: 4E


title: subject_3146

description:
Chip_Id: 1787466047
Chip_Section: 4B


title: subject_3145

description:
Chip_Id: 1787466046
Chip_Section: 3G


title: subject_3384

description:
Chip_Id: 1787466046
Chip_Section: 3E


title: subject_3101_technical rep 2

description:
technical rep 2
Chip_Id: 1787466046
Chip_Section: 3B


title: subject_3183

description:
Chip_Id: 1787466046
Chip_Section: 3A


title: subject_3346_technical rep 2

description:
technical rep 2
Chip_Id: 1787466045
Chip_Section: 2H


title: subject_3373

description:
Chip_Id: 1787466045
Chip_Section: 2E


title: subject_3182

description:
Chip_Id: 1787466045
Chip_Section: 2C


title: subject_3143

description:
Chip_Id: 1787466046
Chip_Section: 3D


title: subject_3418

description:
Chip_Id: 1787466046
Chip_Section: 3H


title: subject_3391

description:
Chip_Id: 1787466046
Chip_Section: 3C


title: subject_3254

description:
Chip_Id: 1787466045
Chip_Section: 2D


title: subject_3132_technical rep 2

description:
technical rep 2
Chip_Id: 1787466045
Chip_Section: 2A


title: subject_3132_technical rep 1

description:
technical rep 1
Chip_Id: 1787466044
Chip_Section: 1H


title: subject_3290

description:
Chip_Id: 1787466046
Chip_Section: 3F


title: subject_3346_technical rep 1

description:
technical rep 1
Chip_Id: 1787466044
Chip_Section: 1G


title: subject_3389

description:
Chip_Id: 1787466045
Chip_Section: 2F


title: subject_3417

description:
Chip_Id: 1787466045
Chip_Section: 2G


title: subject_3235

description:
Chip_Id: 1787466044
Chip_Section: 1F


title: subject_3110

description:
Chip_Id: 1787466044
Chip_Section: 1D


title: mouse resting control

city: Otsu,

first: hirotaka

last: yamamoto

state: Shiga,

address: Tsukinowa, Seta,

country: Japan

institute: Shiga University of Medical Science

hyb_protocol: The two differentially labeled reactions were combined into one tube and the volume was reduced by half  in a SpeedVac® Concentrator. BSA (50mg/ml) was then added to a total volume of 28.5ul. The samples  were incubated with 28.5ul of 2X Enhanced hybridization buffer at 65oC for 10 min and then loaded onto  NCode™ Multi-Species miRNA Microarray V2. The arrays were mounted with the Maui Mixer SL and  hybridized overnight (16-20 h) at 52oC with constant mixing. The washes were performed following the standard protocol recommended in the NCode™ Rapid miRNA  Labeling System Manual.

scan_protocol: The arrays were scanned using a GenePix® 4000B microarray scanner.  (Molecular Devices). The scanned array images were then annotated and analyzed using the GenePix® software.

data_processing: The experiment was performed using a loop design for the data analysis. The annotated data were normalized using a Latin  Squares algorithm by the NCode™ Profiler data analysis software.

label: Alexa Fluor 3

source_name: tibialis anterior muscle, rested.

label_protocol: Into each total RNA sample, 1μl of NCode™ Multi-Species miRNA Microarray Controls (2fmol/ul) was  spiked, and Poly (A) tailing reactions were set up following the protocol recommended in the NCode™  Rapid miRNA Labeling System Manual. The Poly (A) tailed reactions were ligated to labeled DNA polymers by using the 6X Alexa Fluor® 3 (A3)  Rapid Ligation Mix or 6X Alexa Fluor® 5 (A5) Rapid Ligation Mix following the protocol recommended in  the NCode™ Rapid miRNA Labeling System Manual.

extract_protocol: Total RNAs were isolated from C2C12 myocyte or tibialis anterior muscle using TRIZOL reagent according to manufacturer’s manual.

label: Alexa Fluor 5

source_name: myocyte differentiated and stretched

tag: cell line


title: C2C12 undifferentiated

source_name: myocyte undifferentiated

source_name: tibialis anterior muscle, exercised, 7days.


title: mouse exercised 1day

source_name: tibialis anterior muscle, exercised, 1day.


title: C2C12 differentiated

source_name: myocyte differentiated


title: mouse exercised 7day


title: C2C12 stretched


title: subject_3133

description:
Chip_Id: 1787466045
Chip_Section: 2B


title: subject_3181

description:
Chip_Id: 1787466044
Chip_Section: 1C


title: subject_3387

description:
Chip_Id: 1787466044
Chip_Section: 1E


title: subject_3130_technical rep 1

description:
technical rep 1
Chip_Id: 1787466044
Chip_Section: 1B


title: subject_3416

description:
Chip_Id: 1787466044
Chip_Section: 1A


title: Passage 5_Sphere cells (4060001033_C)

status: Public on May 13 2011

city: dayton

first: yiling

last: hong

state: OH

address: 300 college park

department: biology

institute: university of dayton

description:
Mouse fibroblasts
replicate 2

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: MEF cells

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: FVB/N

value: converted sphere cells

tag: passage

value: P 5


title: MEF cells (4060001016_F)

description:
Mouse embryonic fibroblasts
replicate 3

value: PMEF_NL (Neomycin resistant Primary Mouse Embryo Fibroblasts )


title: Passage 15_Sphere cells (1848071039_D)

description:
Mouse fibroblasts
replicate 1


title: MEF cells (4060001033_D)

description:
Mouse embryonic fibroblasts
replicate 1


title: Passage 5_Sphere cells (4060001016_C)

description:
Mouse fibroblasts
replicate 3


title: MES cells_Control_ Pass_1 (1848071039_B)

description:
Mouse embryo_ICM
replicate 2

source_name: MES cells

value: J11 mouse embryonic stem cells (MES)


title: MEF cells (4060001033_A)

description:
Mouse embryonic fibroblasts
replicate 2


title: Passage 15_Sphere cells (1848071039_F)

description:
Mouse fibroblasts
replicate 3


title: Passage 5_Sphere cells (4060001033_F)

description:
Mouse fibroblasts
replicate 1


title: MES cells_Control_ Pass_1 (1848071039_A)

description:
Mouse embryo_ICM
replicate 1


title: Macrophages with parasite 2

city: Lucknow

first: Neeloo

last: Singh

state: Uttar Pradesh

address: Jankipuram Extension Sitapur Road

department: Biochemistry

country: India

institute: Central Drug Research Institute

description: gene expression data from macrophages infected with Leishmania donovani

hyb_protocol: Biotin labelled Crna samples were loaded onto Affymetrix GeneChip Human Genome U133 Plus 2.0 Array and hybridization conducted in Hybridization Oven 640

scan_protocol: Affymetrix GeneChip scanner 3000 was used

data_processing: Microarray Analysis suite 5.0 and GeneChip Operating Software 1.2 of Affymetrix was used

label_protocol: Biotinylated cRNA was prepared as per standard Affymetrix protocol

growth_protocol: Leishmania donovani infected macrophages were grown in M199 medium at 37 degree incubator

extract_protocol: RNA was extracted by TRIZOL as per manufacturer protocol

treatment_protocol: Infected macrophages were treated with IC50 dose of drug monastrol

tag: infection

value: Leishmania donovani

value: macrophage


title: Macrophages with parasite and monastrol 2

description: gene expression data from macrophages infected with Leishmania donovani and treated with monastrol

value: monastrol


title: Macrophages with parasite and monastrol 3

source_name: macrophages infected with Leishmania donovani and treated with monastrol


title: Macrophages with parasite and monastrol 1

value: macrophages infected with Leishmania donovani and treated with monastrol


title: Macrophages with parasite 1

source_name: macrophages infected with Leishmania donovani


title: HEK293T_BACH1-siRNA2_72h_rep2

city: Berlin

first: Hans-Jörg

last: Warnatz

address: Ihnestrasse 63-73

department: Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
Sample name: BACH1_s_2_72
BACH1_s_2_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Stealth siRNA.

hyb_protocol: Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).

scan_protocol: The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.

data_processing: The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package  to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.

source_name: HEK 293T cells, BACH1 knockdown, 72h

label_protocol: Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).

growth_protocol: The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2

extract_protocol: Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.

treatment_protocol: For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.

value: embryonic kidney cell line HEK 293T

tag: sirna transfection

value: siRNA2 HSS100910 (s)

tag: genotype/variation

value: BACH1 knockdown


title: HEK293T_BACH1-siRNA2_72h_rep1

description:
Sample name: BACH1_s_1_72
BACH1_s_1_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Stealth siRNA.


title: HEK293T_mock-transfection_72h_rep1

description:
Sample name: BACH1_m_1_72
MOCK_m_1_0ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after mock transfection without siRNA.

source_name: HEK 293T cells, mock transfection, 72h

value: mock (without siRNA)

value: control


title: HEK293T_mock-transfection_72h_rep2

description:
Sample name: BACH1_m_2_72
MOCK_m_2_0ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after mock transfection without siRNA.


title: HEK293T_mock-transfection_72h_rep3

description:
Sample name: BACH1_m_3_72
MOCK_m_3_0ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after mock transfection without siRNA.


title: HEK293T_BACH1-siRNA1_72h_rep2

description:
Sample name: BACH1_q_2_72
BACH1_q_2_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Qiagen siRNA.


title: HEK293T_BACH1-esiRNA_72h_rep2

description:
Sample name: BACH1_e_2_72
BACH1_e_2_200ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with esiRNA.

value: esiRNA (e)


title: HEK293T_BACH1-esiRNA_72h_rep3

description:
Sample name: BACH1_e_3_72
BACH1_e_3_200ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with esiRNA.


title: HEK293T_BACH1-siRNA1_72h_rep3

description:
Sample name: BACH1_q_3_72
BACH1_q_3_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Qiagen siRNA.


title: HEK293T_BACH1-esiRNA_72h_rep1

description:
Sample name: BACH1_e_1_72
BACH1_e_1_200ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with esiRNA.


title: HEK293T_mock-transfection_24h_rep4

description:
Sample name: BACH1_m_4_24
MOCK_m_4_0ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after mock transfection without siRNA.

source_name: HEK 293T cells, mock transfection, 24h


title: HEK293T_mock-transfection_24h_rep2

description:
Sample name: BACH1_m_2_24
MOCK_m_2_0ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after mock transfection without siRNA.


title: HEK293T_mock-transfection_24h_rep3

description:
Sample name: BACH1_m_3_24
MOCK_m_3_0ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after mock transfection without siRNA.


title: HEK293T_BACH1-siRNA1_72h_rep1

description:
Sample name: BACH1_q_1_72
BACH1_q_1_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Qiagen siRNA.


title: Passage 15_Sphere cells (11848071039_E)

description:
Mouse fibroblasts
replicate 2

tag: strain


title: subject_3116_technical rep 2

description:
technical rep 2
Chip_Id: 1787466052
Chip_Section: 6F

value: Ctr

value: female

value: no


title: HEK293T_BACH1-siRNA2_72h_rep3

description:
Sample name: BACH1_s_3_72
BACH1_s_3_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Stealth siRNA.


title: MES cells_Control_ Pass_1 (1848071039_C)

description:
Mouse embryo_ICM
replicate 3


title: HEK293T_BACH1-esiRNA_24h_rep2

description:
Sample name: BACH1_e_2_24
BACH1_e_2_200ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with esiRNA.

source_name: HEK 293T cells, BACH1 knockdown, 24h


title: HEK293T_BACH1-siRNA1_24h_rep2

description:
Sample name: BACH1_q_2_24
BACH1_q_2_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Qiagen siRNA.


title: HEK293T_BACH1-siRNA2_24h_rep2

description:
Sample name: BACH1_s_2_24
BACH1_s_2_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Stealth siRNA.


title: HEK293T_BACH1-siRNA2_24h_rep1

description:
Sample name: BACH1_s_1_24
BACH1_s_1_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Stealth siRNA.


title: HEK293T_BACH1-esiRNA_24h_rep3

description:
Sample name: BACH1_e_3_24
BACH1_e_3_200ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with esiRNA.


title: HEK293T_BACH1-siRNA1_24h_rep3

description:
Sample name: BACH1_q_3_24
BACH1_q_3_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Qiagen siRNA.


title: MCF-7 + RARalpha siRNA + vehicle rep1 (MD42)

city: Toledo

first: Robert

middle: J

last: Trumbly

address: 3000 Arlington Avenue

department: Biochemistry and Cancer Biology

institute: University of Toledo

description:
Gene expression data from MCF-7cells treated with vehicle and RARalpha siRNA
MD42

hyb_protocol: The cRNA was fragmented to 35-200 bases length using Affymetrix protocols and hybridized to HG U133 Plus 2.0 array set at 45ºC for 16 hours in an Affymetrix GeneChip® Hybridization Oven 640.

scan_protocol: Each GeneChip was then washed and stained with Streptavidin–Phycoerythrin conjugate (SAPE; Invitrogen Corp.) using an Affymetrix Fluidics Station 450 and scanned on a Affymetrix GeneChip scanner.

data_processing: Scanned image files were analyzed using the Gene Chip Operating System Version 1.4 software, and standard thresholding and filtering operations were used.   The data was normalized using house keeping genes. Normalization assumes that for a subset of genes (i.e., housekeeping genes) the ratio of measured expression averaged over the set should be one.

label_protocol: Isolated total RNA was processed as recommended by Affymetrix, Inc. (Santa Clara, CA). In brief, cDNA was synthesized from the total RNA using the Super-Script Double Stranded cDNA Synthesis kit and T7 Oligo (dT) primers. Using the double stranded cDNA as template, biotin labeled cRNA was generated by in vitro transcription (MEGAscript Labeling Kit) reaction.

growth_protocol: Cells were routinely cultured at 37°C and in 5% CO2 in DMEM supplemented with FBS (10%), penicillin (100unit/ml), streptomycin (100μg/ml) and L-glutamine (2mM). Hormone depleted cells were grown in low glucose phenol-red free media supplemented with 5% charcoal-stripped FBS (v/v) and L-glutamine (2mM) for 48 hours before the experiments

extract_protocol: Total RNA was prepared using the RNeasy Mini kit (Qiagen).

treatment_protocol: Cells were plated at 20% confluence in low glucose phenol red free medium supplemented with 5% charcoal stripped FBS and glutamine 24h-48h prior to transfection. Treatment with vehicle, OH-Tam (100nM), or OH-Tam (500nM) was begun an additional 24h later. Cells were transfected with control siRNA, ERα siRNA or RARα siRNA in 24 well microplates (2.5pmol/well) or 25cm2 flasks (31.25pmol per flask) using 2μl and 12.5 μl of Dharmafect 1 (Thermo Scientific Dharmacon Inc., Lafayette, CO), respectively, according to the vendor’s protocol. The cell culture medium was not replenished for the duration of the experiment.

value: MCF-7 breast cancer cell line

tag: sirna

value: RARalpha siRNA

tag: agent

value: control (vehicle)

tag: dose


title: HEK293T_BACH1-siRNA1_24h_rep1

description:
Sample name: BACH1_q_1_24
BACH1_q_1_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Qiagen siRNA.

tag: time


title: HEK293T_mock-transfection_24h_rep1

description:
Sample name: BACH1_m_1_24
MOCK_m_1_0ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after mock transfection without siRNA.


title: MCF-7 +scrambled siRNA + vehicle rep2 (MD40)

description:
Gene expression data from MCF-7cells treated with vehicle and scrambled siRNA
MD40

value: control (scrambled siRNA)


title: HEK293T_BACH1-siRNA2_24h_rep3

description:
Sample name: BACH1_s_3_24
BACH1_s_3_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Stealth siRNA.


title: Macrophages with parasite 3

description: gene expression data from macrophages infected with Leishmania donovani

tag: sample type

value: Leishmania donovani

tag: cell type


title: WT+Cre_2

city: Stanford

first: Dadi

last: Jiang

address: 269 Campus Drive, CCSR-South 1240

institute: Stanford University

hyb_protocol: Affymetrix oligonucleotide array standard protocol

data_processing: BRB-ArrayTools v3.8.1 & RMA

source_name: Mouse Embryonic Fibroblast

extract_protocol: Qiagen RNeasy Kit

value: mouse embryonic fibroblast

tag: genotype

tag: transgene

value: retroviral H-Ras V12 mutant

tag: background strain


title: WT+Cre_1

scan_protocol: Affymetrix oligonucleotide array standard protocol


title: HEK293T_BACH1-esiRNA_24h_rep1

description:
Sample name: BACH1_e_1_24
BACH1_e_1_200ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with esiRNA.


title: Null+Cre_4

label_protocol: Affymetrix oligonucleotide array standard protocol

value: p53_null knock-in+Adeno-Cre


title: WT+Cre_3

value: 129/Sv/C57BL6 mixed


title: MCF-7 +scrambled siRNA + vehicle rep1 (MD39)

description:
Gene expression data from MCF-7cells treated with vehicle and scrambled siRNA
MD39


title: Null+Cre_3


title: Null+Cre_2


title: LSL-WT+Emp_2

value: p53_LSL-WT knock-in+Adeno-Empty


title: MCF-7 +scrambled siRNA + 500 nM 4-hydroxytamoxifen rep2 (MD36)

description:
Gene expression data from MCF-7cells treated with 500 nM 4-hydroxytamoxifen and scrambled siRNA
MD36


title: LSL-WT+Cre_2

value: p53_LSL-WT knock-in+Adeno-Cre


title: LSL-WT+Emp_3


title: MCF-7 +ER siRNA + vehicle rep2 (MD38)

description:
Gene expression data from MCF-7cells treated with vehicle and ER siRNA
MD38

value: ER siRNA


title: MCF-7 +scrambled siRNA + vehicle rep2 (MD32)

description:
Gene expression data from MCF-7cells treated with vehicle and scrambled siRNA
MD32


title: LSL-QM+Cre_3

value: p53_LSL-QM knock-in+Adeno-Cre


title: MCF-7 +ER siRNA + vehicle rep1 (MD37)

description:
Gene expression data from MCF-7cells treated with vehicle and ER siRNA
MD37


title: junctional zone of HSD rat placenta, biological rep3

city: Bunkyou-ku

first: Toshihiro

last: Konno

state: Tokyo

address: Yayoi 1-1-1

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

description: Gene expression data from junctional zone of placenta in Holtzman-Sprague Dawley rat strains at gestation day 18.5

hyb_protocol: RNA samples were hybridized to Affymetrix Rat 230 2.0 DNA microarray chips using the GeneChip® Hybridization Oven 640 (Affymetrix, Santa Clara, CA). Washing and staining of the hybridized chips were conducted using the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Chips were scanned using the Affymetrix GeneChip® Scanner 3000 (Affymetrix) with autoloader.

data_processing: Expression data sets were analyzed using the R statistics software (http://www.r-project.org/) with BioConductor software (http://www.bioconductor.org/) packages.  The MAS5 method from the BioConductor software was used for background correction, normalization, and summarization of the DNA microarray data.

organism: Rattus norvegicus

source_name: Junctional zone of placenta in Holtzman-Sprague Dawley rat strain

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: Virgin female rats 8–10 wk of age for each strain were cohabited with adult males (>3 mo of age) of the same strain. Mating was assessed by daily inspection of vaginal lavages. The presence of sperm in the vaginal lavage was considered as day 0.5 of pregnancy.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified by spectrophotometry and quality was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies,  Santa Clara, CA).

treatment_protocol: On gestation day 18.5, female rats were sacrificed and placentation sites collected. Junctional zone tissues were dissected from placenta under dissection microscope and snap frozen in liquid nitrogen.

tag: tissue

value: junctional zone of placenta

value: Holtzman-Sprague Dawley

tag: gestational stage

value: day 18.5 of pregnancy


title: LSL-WT+Cre_1


title: PEO4 Placebo Control rep3

city: Aurora

first: Monique

last: Spillman

state: CO

address: Mail Stop B198-4, PO Box 6511

institute: University of Colorado Denver

hyb_protocol: Samples were hybridized to U133 2+ whole human genome expression arrays in the University of Colorado Comprehensive Cancer Center Microarray Core according to their standard protocol

scan_protocol: Samples were scanned in the University of Colorado Comprehensive Cancer Center Microarray Core according to their standard protocol

data_processing: Samples were assayed for quality and to check for MAS 5.0 present calls on at least one chip using R and then RMA normalized and analyzed using Partek

source_name: PEO4 (ER+) ovarian cancer cells tagged with ZsGreen and laser captured from intraperitoneal xenografts of a mouse treated with placebo

label_protocol: RNA was amplified with WT-Ovation FFPE RNA Amplification System V2 (NuGEN, San Carlos, CA ) and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (NuGEN)

extract_protocol: RNA was isolated from the laser captured human cells using the Picopure RNA Isolation kit (Molecular Devices)

value: PEO4 (ER+) ovarian cancer cells

tag: protocol

value: human ovarian cancer cells xenografted into female ovariectomized athymic nude mice

value: Placebo


title: junctional zone of HSD rat placenta, biological rep2


title: MCF-7 +scrambled siRNA + 100 nM 4-hydroxytamoxifen rep1 (MD33)

description:
Gene expression data from MCF-7cells treated with 100 nM 4-hydroxytamoxifen and scrambled siRNA
MD33

tag: cell line

value: MCF-7 breast cancer cell line


title: LSL-WT+Emp_1


title: MCF-7 +scrambled siRNA + vehicle rep1 (MD31)

description:
Gene expression data from MCF-7cells treated with vehicle and scrambled siRNA
MD31

value: control (scrambled siRNA)

value: control (vehicle)


title: MCF-7 +scrambled siRNA + 500 nM 4-hydroxytamoxifen rep1 (MD35)

description:
Gene expression data from MCF-7cells treated with 500 nM 4-hydroxytamoxifen and scrambled siRNA
MD35


title: MCF-7 +scrambled siRNA + 100 nM 4-hydroxytamoxifen rep2 (MD34)

description:
Gene expression data from MCF-7cells treated with 100 nM 4-hydroxytamoxifen and scrambled siRNA
MD34


title: LSL-QM+Cre_2

value: mouse embryonic fibroblast


title: Wild-type control 4

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

description: RMA expression value derived from Expression Console software

hyb_protocol: Hybridization protocol 10 ug of fragmented cRNA was hybridized to each array for 17 hours at 45°C with rotation at 60rpm according to the Affymetrix standard protocol.

scan_protocol: Mouse Exon 1.0 ST Affymetrix arrays were scanned using the GeneChip Scanner 3000.

data_processing: Microarray data were initially processed using GeneChip Operating Software. DTT data were transferred by Transfer Tool software (Affymetrix). Chip quality and raw microarray data pre-processing were performed according to the Affymetrix guidelines using Expression Console software. The following parameters were checked on the arrays: mean signal, mean background signal and comparison of signal values from the positive controls to the negative. After background subtraction, the data were processed using RMA (All: RMA-Sketch) method and quantile normalization.

label_protocol: 1 ug of total RNA was processed using a ribosomal RNA reduction step (RiboMinus Kit, Invitrogen) and labeled according to the Whole Transcriptome Sense Kit (Affymetrix).

growth_protocol: Experiments were performed on three-month old wild-type (C57BL/6) or neuropsin-/- mice backcrossed to C57BL/6 for 12 generations. Animals were housed three to five per cage in a colony room with a 12 hour light/dark cycle (lights on at 7AM) with ad libitum access to commercial chow and tap water. The experiments were approved by the UK Home Office and the UoL Ethical Committee.

extract_protocol: Amygdalae tissue have been submerged in RNAlater solution (Qiagen) and stored at -20°C until RNA purification. Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen) as per manufacturer's instructions. The rybosomal fraction of RNA was significantly reduced with RiboMinus Kit (Invitrogen) and the RNA integrity has been verified by electrophoresis using Agilent Bioanalyser 2100.

value: Wild-type

value: brain amygdala

tag: genetic background


title: junctional zone of BN rat placenta, biological rep3

description: Gene expression data from junctional zone of placenta in Brown Noway rat strains at gestation day 18.5

source_name: Junctional zone of placenta in Brown Noway rat strain

value: Brown Norway


title: LSL-WT+Cre_3

value: retroviral H-Ras V12 mutant

value: 129/Sv/C57BL6 mixed


title: junctional zone of BN rat placenta, biological rep2


title: PEO4 Placebo Control rep2


title: Neuropsin-/- knock-out 1

value: Neuropsin-/- knock-out


title: LSL-QM+Cre_1

value: p53_LSL-QM knock-in+Adeno-Cre


title: LSL-53,54+Cre_4

value: p53_LSL-53,54 knock-in+Adeno-Cre


title: PEO4 Placebo Control rep1


title: PEO4 Estrogen Tx rep4

source_name: PEO4 (ER+) ovarian cancer cells tagged with ZsGreen and laser captured from intraperitoneal xenografts of a mouse treated with estrogen

value: Estrogen


title: Neuropsin-/- knock-out 3


title: junctional zone of BN rat placenta, biological rep1

value: junctional zone of placenta

value: day 18.5 of pregnancy


title: LSL-53,54+Cre_3


title: 2008 Estrogen Tx rep4

source_name: 2008 (ER-) ovarian cancer cells tagged with ZsGreen and laser captured from intraperitoneal xenografts of a mouse treated with estrogen

value: 2008 (ER-) ovarian cancer cells

value: human ovarian cancer cells xenografted into female ovariectomized athymic nude mice


title: Neuropsin-/- knock-out 5


title: FPP accumulation-LB-29.5hr-2

city: Emeryville

last: Dahl

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

description: Technical replicate 2 of 3

hyb_protocol: Kizer, L., et al., 2008.  Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production. Appl. Environ. Microbiol. 74: 3229-3241.

scan_protocol: Arrays were scanned with an Axon 4200 scanner acquiped with GenePix Pro6.0

data_processing: Feature fluorescence intensities [F532 media-B532 and F635media-B635] were extracted with GenePix Pro6.0.  Local hybridization and intensity-dependent artifacts were removed with Lowess normalization using Standardization and Normalization of Microarray Data (SNOMAD, http://pevsnerlab.kennedykrieger.org/snomadinput.html).  The three replicate spots for each gene were averaged and variance calculated.

organism: Escherichia coli DH1

source_name: FPP (pMBIS/pADSmut, 29.5 hr0

growth_protocol: Individual clones of E. coli DH1 transformed with pMBIS/pADS or pMBIS/pADSmut were grown in 100 mL LB in 1 L flasks.  At OD ~ 0.3, 10 mM mevalonate and 0.5 mM IPTG were added to each culture.

extract_protocol: Biomass was snap frozen in liquid nitrogen and stored at -80 C prior to extraction with Qiagen Rneasy Midi kits.  RNA integrity was verified with a 2100 Bioanalyzer (Agilent)

treatment_protocol: The strain accumulating FPP (pMBIS/pADSmut) is considered the treatment while the strain producing the non-toxic amorphadiene is considered the control.

tag: treatment

value: 10 mM Mevalonate and 0.5 mM IPTG added

source_name: amorphadiene (pMBIS/pADSmut, 29.5 hr)


title: FPP accumulation-LB-29.5hr-1

description: Technical replicate 1 of 3

label_protocol: Kizer, L., et al., 2008.  Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production. Appl. Environ. Microbiol. 74: 3229-3241.

source_name: amorphadiene (pMBIS/pADS, 29.5 hr)


title: MCF-7 + RARalpha siRNA + vehicle rep1 (MD41)

description:
Gene expression data from MCF-7cells treated with vehicle and RARalpha siRNA
MD41

value: MCF-7 breast cancer cell line

value: RARalpha siRNA


title: FPP accumulation-LB-7hr-1

description: Technical replicate 1 of 3

source_name: FPP (pMBIS/pADSmut, 7 hr0

source_name: amorphadiene (pMBIS/pADS, 7 hr)


title: Neuropsin-/- knock-out 4


title: FPP accumulation-LB-7hr-2

description: Technical replicate 2 of 3


title: Wild-type control 1


title: Wild-type control 3


title: FPP accumulation-LB-5hr-3

description: Technical replicate 3 of 3

source_name: FPP (pMBIS/pADSmut, 5 hr0

source_name: amorphadiene (pMBIS/pADS, 5 hr)


title: FPP accumulation-LB-5hr-1

description: Technical replicate 1 of 3


title: FPP accumulation-LB-5hr-2

description: Technical replicate 2 of 3


title: LSL-25,26+Cre_5

value: mouse embryonic fibroblast

value: p53_LSL-25,26 knock-in+Adeno-Cre


title: 2008 Estrogen Tx rep3


title: FPP accumulation-LB-2.5hr-3

description: Technical replicate 3 of 3

source_name: FPP (pMBIS/pADSmut, 2.5 hr0

source_name: amorphadiene (pMBIS/pADS, 2.5 hr)


title: LSL-25,26+Cre_4


title: LSL-25,26+Cre_2


title: 2008 Placebo Control rep3

source_name: 2008 (ER-) ovarian cancer cells tagged with ZsGreen and laser captured from intraperitoneal xenografts of a mouse treated with placebo

value: Placebo


title: 2008 Placebo Control rep4


title: LSL-53,54+Cre_2


title: FPP accumulation-LB-2.5hr-1

description: Technical replicate 1 of 3


title: 2008 Placebo Control rep2


title: PEO4 Estrogen Tx rep3

value: PEO4 (ER+) ovarian cancer cells


title: FPP accumulation-LB-2.5hr-2

description: Technical replicate 2 of 3


title: Wild-type control 2

value: Wild-type

value: brain amygdala


title: Heregulin 979-CLA-34

city: Nashville

first: Ritwik

last: Ghosh

state: TN

address: 2220 Pierce Avenue, 777 PRB

institute: Vanderbilt University

description: Gene expression data from cells treated with Heregulin for 48 hours

hyb_protocol: 5.5 ug biotinylated cRNA was fragmented and hybridizied to an Affymetrix Genechip Human Gene 1.0 ST array

scan_protocol: Hybridized cRNA was detected using streptavidin coupled to phycoerythrin. Genechips were scanned using Genechip Scanner 3000 7G Plus 2 and Genechip Operating System (Affymetrix)

data_processing:
Default values were used to grid images (.DAT) and generate .CEL and .CHP files.
RMA

source_name: MCF10A-HER2-FKBP-HA cells

label_protocol: GeneChip One-Cycle Target Labeling and Control reagents kit (Affymetrix)

growth_protocol: Cells are maintained in DMEM/F12 + 5% horse serum + 20ng/ml EGF + 100ng/ml cholera toxin + 500ng/ml hydrocortisone + 10microgram/ml insulin

extract_protocol: RNA extracted using Ambion ToTALLY RNA kit

treatment_protocol: Cells were seeded in 100 mm dishes in triplicate. 24 hours before ligand treatment, media was changed to DMEM/F12 + 100ng/ml cholera toxin + 500ng/ml hydrocortisone + 10microgram/ml insulin. RNA was harvested 48 hours after addition of ligand.

value: normal breast cell line with stably transfected full-length chimeric human HER2 receptor with FKBP and HA tags

value: Heregulin


title: Wild-type control 5


title: Heregulin 979-CLA-36


title: Heregulin 979-CLA-35


title: PEO4 Estrogen Tx rep2


title: LSL-25,26+Cre_3

source_name: Mouse Embryonic Fibroblast

value: retroviral H-Ras V12 mutant

value: 129/Sv/C57BL6 mixed


title: 2008 Estrogen Tx rep2

value: Estrogen


title: 2008 Estrogen Tx rep1


title: TGF-alpha 979-CLA-33

description: Gene expression data from cells treated with TGF-alpha for 48 hours

value: TGF-alpha


title: TGF-alpha 979-CLA-31


title: TGF-alpha 979-CLA-32


title: Untreated 979-CLA-27

description: Gene expression data from untreated cells

value: Untreated


title: AP1510 979-CLA-28

description: Gene expression data from cells treated with AP1510 for 48 hours


title: Untreated 979-CLA-26


title: LSL-25,26+Cre_1


title: AP1510 979-CLA-30


title: AP1510 979-CLA-29


title: 2008 Placebo Control rep1

value: 2008 (ER-) ovarian cancer cells

value: human ovarian cancer cells xenografted into female ovariectomized athymic nude mice


title: PEO4 Estrogen Tx rep1


title: Untreated 979-CLA-25


title: junctional zone of HSD rat placenta, biological rep1

source_name: Junctional zone of placenta in Holtzman-Sprague Dawley rat strain

value: junctional zone of placenta

value: Holtzman-Sprague Dawley

value: day 18.5 of pregnancy


title: Stored storage root_technical_repeat_2

city: Shanghai

first: Jun

last: Yang

address: 300 Fenglin Road

country: China

institute: SIPPE

hyb_protocol: Arrays were incubated at 65 °C for 17 h in Agilent hybridization chambers (G2545A) and then washed according to the Agilent protocol at room temperature.

scan_protocol: Hybridized microarray slides were scanned at 5-μm resolution with an Agilent Technologies Scanner (G2505B), and images were saved in JPG format. Both 10% and 100% Photomultiplier tube (PMT) settings were selected, and combined images were exported.

data_processing: The signal intensities of all spots on each image were quantified by Agilent Feature Extraction software, and data were saved as.txt files for further analysis. Quantile normalization.

organism: Manihot esculenta

source_name: Stored cassava storage root slice

label_protocol: RNA labeling was conducted by the Shanghai Biochip Corporation (Shanghai) following the manufacturer’s protocol of Agilent Technologies

growth_protocol: The cultivar TMS60444, which is frequently used for genetic engineering, was employed in the present study. The in vitro plants were transferred to pots for one month of growth in a greenhouse and then planted in a field.

extract_protocol: Total RNA was extracted from root samples, including fibrous root (FR), developing storage root (DR), mature storage root (MR) and technical repeats (TR), using the RNeasy® Mini Kit (Qiagen). RNA quality was checked on a 1% agarose gel using an RNase-free electrophoresis system.

treatment_protocol: Fibrous roots (FR), developing storage roots (DR) and mature storage roots (MR) were collected from three independent healthy 4 month-old cassava plants in the field and submerged into liquid nitrogen immediately. All samples were maintained in liquid nitrogen during transportation, and they were stored in an ultra-freezer (-80°C) until RNA extraction.

tag: developmental stage

value: Storage root

value: root

tag: cultivar


title: Thapsigargin_3h_rep2

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description: Gene expression data from Daoy human medulloblastoma cells treated for 3h with 1uM thapsigargin.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Daoy medulloblastoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum, 2mM glutamine and 1% antibiotic-antimycotic at 37ºC in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini-prep kit according to the manufacturer’s protocol.

treatment_protocol: Cells were plated and left untreated (control) or treated with thapsigargin (1uM) for 3h or 8h.

value: Thapsigargin


title: Stored storage root_technical_repeat_1


title: Thapsigargin_8h_rep2

description: Gene expression data from Daoy human medulloblastoma cells treated for 8h with 1uM thapsigargin.


title: Thapsigargin_8h_rep1


title: Mature_root_3

source_name: Cassava mature storage root

value: Mature storage root


title: Thapsigargin_3h_rep1


title: Control_rep2

description: Gene expression data from untreated Daoy human medulloblastoma cells.

value: Control


title: Mature_root_2


title: Control_rep1


title: Benzo[a]pyrene (1uM) rep 2

city: Newcastle

first: Alexander

middle: Peter

last: Sobinoff

state: NSW

address: University Drive

department: Science and IT

country: Australia

institute: University of Newcastle Australia

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using BioConductor's lumi package in R statistical software

source_name: Neonatal mouse ovaries cultured in Benzo[a]pyrene (1uM)

label_protocol: Biotinylated cRNA were prepared with Ambion's Illumina RNA Amplification kit for Illumina arrays

growth_protocol: Swiss neonates were sacrificed by CO2 inhalation followed by decapitation. Ovaries were excised, trimmed of excess tissue and placed on culture plate inserts in 6-well tissue culture plate wells floating atop 1.5ml DMEM/F12 medium containing 5% (v/v) fetal calf serum, 1mg/ml bovine serum albumin, 50µg/ml ascorbic acid, 27.5μg/ml insulin–transferrin–selenium, 2.5 mM glutamine and 5U/ml penicillin/streptomycin. Media were supplemented with 40 ng/ml basic fibroblast growth factor, 50 ng/ml leukemia inhibitory factor, and 25 ng/ml stem cell factor. Using fine forceps a drop of medium was placed over the top of each ovary to prevent drying. Ovaries were cultured for 4 days at 37°C and 5% CO2 in air, with media changes every two days.

extract_protocol: Total RNA was isolated from ovaries using two rounds of a modified acid guanidinium thiocyanate–phenol–chloroform protocol: washed cells resuspended in lysis buffer (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarkosyl, 0.72% β-mercaptoethanol). RNA was isolated by phenol/chloroform extraction and isopropanol precipitated.

treatment_protocol: Ovaries were treated with vehicle control medium (0.01% Acetone), DMBA (50nM) or BaP (1uM). DMBA culture concentration was determined by pilot studies performed in our laboratory with the intention of inducing overt toxicity.

value: Ovary

tag: age

value: Post natal day 3-4

value: Benzo[a]pyrene 1uM

tag: strain

value: Swiss


title: Slide 176969

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Avarage ratio of inter slide replicates

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (15, 18, 49). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: 0.2mM Zn {A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences)

growth_protocol: Cells were grown to OD600 of 0.25 in CDM medium with and without 0.2 Mm Zn

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006; Shafeeq et al., 2011). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

source_name: 0mM Zn {B}


title: Developing_root_3

source_name: Cassava developing storage root

value: Developing storage root


title: Slide 176968

description: Avarage ratio of inter slide replicates


title: Benzo[a]pyrene (1uM) rep 1


title: Neuropsin-/- knock-out 2

value: Neuropsin-/- knock-out

value: brain amygdala


title: Benzo[a]pyrene (1uM) rep 3


title: Mature_root_1


title: Developing_root_2


title: Slide 176967

description: Avarage ratio of inter slide replicates


title: Fibrous_root_3

source_name: Cassava fibrous root

value: Fibrous root


title: Slide 185511

description: Avarage ratio of inter slide replicates

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

source_name: mutant {A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences

growth_protocol: Cells were grown to OD600 of 0.25 in CDM medium with 0.2 Mm Zn

source_name: wild-type {B}


title: H520 nascent strand DNA, NS55

type: genomic

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

description: Nascent strand prep of H520

hyb_protocol: The hybridization protocol followed was essentially similar to one used for comparative genomic hybridization (CGH) to NimbleGen arrays (NimbleGen Systems Inc.). The test DNA consisted of the pooled DNA fractions containing nascent strands in the 0.7-1.5 kb size range. The reference DNA sample, corresponded to DNA obtained from the same cell line from which the nascent strand preparation was originated. This DNA was sheared by sonication to yield an equivalent range in size fragments as the test DNA

scan_protocol: Scanned on an Agilent G2565AA scanner. Image Analysis Software: NimbleScan v2.1.

data_processing: No background subtraction, no nonlinear normalization algorithm was applied.

molecule: genomic DNA

label_protocol: Each of the DNA samples was independently labeled with unique dye-modified dUTPs (e.g. Cy5- or Cy3-), and then combined before hybridization to a NimbleGen array using the MAUI hybridization system at 42°C for 16-20 hrs. The slide containing the array was then removed from the MAUI hybridization chamber while immersed in wash buffer I (1X SSC, 0.05% SDS), placed in slide rack containing wash buffer I and washed twice in the same buffer for 5 min with agitation. The slide was transferred to wash buffer II (0.1X SSC) and the washing repeated as before. The slide was then removed from the slide rack, dried by centrifugation (1500 rpm for 3 min), loaded in a cassette, and scanned

extract_protocol: For the isolation of short nascent DNA from human cell lines a procedure employed in our laboratory (reference below) was followed with minor modifications. About 108 cells were washed in PBS and collected by centrifugation. Cells were lysed with SDS in presence of Proteinase K, DNA extracted with phenol and chloroform, precipitated by centrifugation with ethanol in 0.3M Sodium Acetate, and resuspended in TE (10mM Tris-HCl, pH 8.0; 1mM EDTA) buffer. The re-suspended DNA was denatured by incubation in boiling water for 12 min, followed by quenching in ice for 6 min, and applied onto to a 5-30% neutral sucrose gradient. After centrifugation of the gradient in a SW28 Beckman rotor for 24,000 rpm for 20 hrs at 15°C, the gradient was fractionated using an ISCO 185 fractionator. I ml fractions were collected and the linearity of the gradient assessed by measuring the refractive index of every third fraction. Only gradients with a regression line R2 value larger than 0.99 were further processed. The consistency of the gradients allowed us to identify fractions corresponding to the desired DNA size range, which in our experience falls around a refractive index of 1.35.  About 80 ul of every gradient fraction was concentrated 10-fold in a speedvac and analyzed by gel electrophoresis in 1% agarose to confirm the fragment size range in the fractions. Fractions containing nascent DNA strands in the range of 0.7-1.5kb in length were pooled and dialyzed. The quality and abundance of short nascent strands in our nascent DNA preparation was assessed by real time PCR, and used for hybridization to DNA tiling microarrays.  Reference: Hu, L., Xu, X., and Valenzuela, M.S. Initiation sites for human DNA replication at a putative ribulose-5-phosphate-3-epimerase gene. Biochem. Biophys. Res. Commun. 320:648-655 (2004)

tag: H520, Human lung squamous carcinoma cell line

source_name: H520 DNA

extract_protocol: The reference DNA sample, corresponded to DNA obtained from the same cell line from which the nascent strand preparation was originated, was extracted according to arrayCGH protocol. This DNA was sheared by sonication to yield an equivalent range in size fragments as the test DNA.


title: 7,12-dimethylbenz-[a]anthracene (50nM) rep 1

source_name: Neonatal mouse ovaries cultured in 7,12-dimethylbenz-[a]anthracene (50nM)

value: 7,12-dimethylbenz-[a]anthracene 50nM


title: Developing_root_1


title: Fibrous_root_2


title: Synchronous prep of MCF7 nascent strand DNA, NS24

description: replicate of nascent strand prep of synchronous MCF7 cells

tag: MCF7, Human breast cancer cell line

source_name: MCF7 DNA


title: 7,12-dimethylbenz-[a]anthracene (50nM) rep 2


title: 7,12-dimethylbenz-[a]anthracene (50nM) rep 3


title: Slide 185503

description: Avarage ratio of inter slide replicates


title: MCF7 ChIP-chip of Pol-II

description: ChIP of Pol-II

extract_protocol: Chromatin immunoprecipitation.(ChIP) was carried out according to standard protocols   using a ChIP-IT kit from Active Motif (Carlsbad, CA), and following the manufacture’s instructions with minor modifications.  Briefly, MCF7 cells were crosslinked with 1% formaldehyde at room temperature for 15 minutes.  Then the cells were sheared with a VirSonic 100 sonicator for 10 cycles of ten 1-second pulses. After centrifugation, the chromatin contained in the supernatant was collected. Part of it was set aside and served as input fraction. The rest  was immunoprecipitated overnight at 4°C. The antibodies used were:  anti-polymerase II antibody (Upstate 05-623) and anti-trimethylated histone H3K4 (Abcam Ab8580). After reversal of crosslinking at 65°C overnight, the ChIP DNA was purified using spin columns provided by the kit.  For ChIP-chip, the ChIP DNA was amplified using the ligation mediated-PCR method as described in the reference below.   A second round amplification of 15 cycles was added to increase the yield of DNA.  3 ?g of amplified ChIP DNA and Input DNA was labeled with Cy5–dUTP and Cy3-dUTP, respectively, with BioPrime DNA Labeling System (Invitrogen).  The labeled ChIP DNA and Input DNA were then combined and hybridized to the NimbleGen arrays. Reference: Li et al. (2003) A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells  Proc Natl Acad Sci U S A 100(14): 8164-9

source_name: MCF7 ChIP input DNA


title: MCF7 ChIP-chip of H3K4Me3, replicate

description: replicate of ChIP of H3K4Me3


title: Control (0.01% Acetone) rep 3

source_name: Neonatal mouse ovaries cultured in Acetone (0.01%)

value: Control 0.01% Acetone


title: MCF7 ChIP-chip of H3K4Me3

description: ChIP of H3K4Me3


title: H520 nascent strand DNA, NS58, replicate

description: replicate of nascent strand prep of H520


title: 13969472 - Plus IND 3 vs Minus IND 3

status: Public on May 12 2011

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

institute: INRA

description:
arabidopsis thaliana (columbia)  - age: 8day dev.stage (Boyes et al. Plant Cell 2001):boyes: 1.02
Identification of miRNAs regulated by IND

hyb_protocol: Minus IND 3 Cy5 / Plus IND 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Minus IND 3

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - Media: MS liquid  hygrometry: seedlings growing in liquid  Temperature: 21C  Light: 16h

extract_protocol: Minus IND 3:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Mock - compound based treatment - compound addition,mock induction:.

tag: ecotype

value: Columbia

tag: induction

value: control

value: seedling

source_name: Plus IND 3

extract_protocol: Plus IND 3:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Dexamethasone - compound based treatment - compound addition,dexamethasone:.

value: InD


title: Control (0.01% Acetone) rep 1


title: 13912510 - adg1 N3 vs WS N3

description: What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves.

hyb_protocol: WS N3 Cy5 / adg1 N3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias in R version 2.8.1 (2008-12-22) (ISBN 3-900051-07-0). Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

source_name: WS N3

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - Media: peat-based compost Hygrometry: approximately 60% during the day Temperature: 22°C during the day/ 17°C during the night Light: 16h light

extract_protocol: WS N3:6ug.

treatment_protocol: no treatment

value: wassilewskija

tag: genotype/variation

value: wild type

source_name: adg1 N3

value: mutant (adg1-)


title: 13969299 - Minus IND 2 vs Plus IND 2

hyb_protocol: Plus IND 2 Cy5 / Minus IND 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Plus IND 2

extract_protocol: Plus IND 2:10ug. (Qiagen_RNeasy.pdf)

source_name: Minus IND 2

extract_protocol: Minus IND 2:10ug. (Qiagen_RNeasy.pdf)


title: 13969298 - Plus IND 1 vs Minus IND 1

hyb_protocol: Minus IND 1 Cy5 / Plus IND 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Minus IND 1

extract_protocol: Minus IND 1:10ug. (Qiagen_RNeasy.pdf)

source_name: Plus IND 1

extract_protocol: Plus IND 1:10ug. (Qiagen_RNeasy.pdf)


title: Control (0.01% Acetone) rep 2

value: Ovary


title: 13969453 - Minus IND 3 vs Plus IND 3

hyb_protocol: Plus IND 3 Cy5 / Minus IND 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: BT474 nascent strand DNA, NS50

description: Nascent strand prep of BT474

tag: BT474, Human breast cancer cell line

source_name: BT474 DNA


title: 13969297 - Minus IND 1 vs Plus IND 1

hyb_protocol: Plus IND 1 Cy5 / Minus IND 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Fibrous_root_1

source_name: Cassava fibrous root

value: root