title: C.elegans hydrogen sulfide sample replicate 2

source_name: C.elegans hydrogen sulfide exposure, replicate 2


title: C.elegans control sample replicate 1

status: Public on Jul 30 2013

type: RNA

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

description: Standard affymetrix recommended quality control parameters were used during entire experiment.

hyb_protocol: 10 μg of Biotin end labeled aRNA (amplified RNA) was fragmented and hybridized to the Affymetrix C. elegans GeneChips as recommended by Affymetrix. The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G), as well as for the preliminary data analysis.

data_processing:
Preprocessing of microarray raw data including probe-specific background correction, summarization of probe set values, and normalization was carried out using the GCRMA algorithm with CARMAweb 1.4, an R and Bioconductor based web service for microarray data analysis (Rainer et al., 2006).
Rainer J, Sanchez-Cabo F, Stocker G, Sturn A, Trajanoski Z (2006). CARMAweb: comprehensive R and Bioconductor based web service for microarray data analysis. Nucleic Acids Res 34:W498–W503

label: biotin

molecule: total RNA

organism: Caenorhabditis elegans

source_name: C.elegans control exposure, replicate 1

label_protocol: 200 ng of total RNA was subjected to aRNA amplification and Biotin labeling as described in the MessageAmpTM Premier RNA Amplification Kit (Ambion) for microarray analysis. aRNA cleanup was achieved using magnetic beads (Ambion).

growth_protocol: Caenorhabditis elegans were exposed (for 48h in liquid medium followed by a further 12h on plates containing nematode growth medium, NGM) to the slow releasing H2S donor drug, GYY4137 (morpholin-4-ium 4 methoxyphenyl (morpholino) phosphinodithioate, 100 uM).

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).

tag: age

value: larvae (L4)

tag: tissue

value: whole animal

tag: strain

value: N2 (Bristol)


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_ms1_mutant_sample1

city: Tsukuba

first: Norihiro

last: Futamura

state: Ibaraki

address: 1 Matsunosato

country: Japan

institute: Forestry and Forest Products Research Institute (FFPRI)

description: This RNA sample was collected from male strobili of a male-sterile mutant no. 17 derived from Toyama 1 half-sib F2 pedigree on September 18th, 2005. It is the first of seven sterile male strobilus samples with pre-meiotic stage of pollen development .

hyb_protocol: Hybridization was performed by Roche NimbleGen Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) and quantile normalization (Bolstad et al. Bioinformatics 19(2):185). Arrays devived from individual samples and pooled samples were normalized separately.

organism: Cryptomeria japonica

source_name: Cryptomeria japonica ms1 mutant 17

label_protocol: Labeling was performed by Roche NimbleGen Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
Trees, from 4 to 6 years old, were treated with 100 ppm gibberellic acid GA3 at the end of July to induce flowering. Male strobili of male-fertile (MF) and male-sterile (MF) Cryptomeria japonica were collected at seven-days intervals from September to November.
The collected male strobili were observed by light microscopy, and classified into four types: pre-meiosis (PM) stage, meiosis (MEI) stage, tetrad (TET) stage and uninuclear microspore (UM) stage, according to their stage of pollen development.

extract_protocol: Total RNA was extracted using the a modified CTAB method (Futamura et al. BMC Genomics 9(1): 383) and purified with the SV Total RNA Isolating Sysytem (Promega, Madison, WI, USA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

tag: genotype

value: Toyama ms1 mutant

tag: phenotype

value: male sterile

tag: accession

value: male strobili with pre-meiotic stage of pollen development


title: 566_N.lepida_control_LR

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

country: USA

institute: University of Utah

description: AID 566, Neotoma lepida, control rabbit chow diet, Lytle Ranch, liver tissue

hyb_protocol: Standard Agilent 1-color gene expression hybridization protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing:
Images from scanned arrays were processed with Agilent Feature Extraction software version 10.5.1.1.
Data files were filtered to remove features flagged as nonuniform features or population outliers. Remaining intensity values for each probe were averaged, to yield single value for each unique probe sequence.
Intensity values were log base 2 transformed and normalized by median centering.

organism: Neotoma lepida

label_protocol: Agilent One-Color Quick Amp Labeling Kit

extract_protocol: Ambion RNAqueous (RNA extraction)

treatment_protocol: RNAlater (Sigma)

tag: population

value: Lytle Ranch

tag: gender

value: male

tag: diet

value: control: rabbit chow

value: liver


title: 546_N.lepida_control_LR

description: AID 546, Neotoma lepida, control rabbit chow diet, Lytle Ranch, liver tissue

value: female


title: 308_N.bryanti_control_PS

description: AID 308, Neotoma bryanti, control rabbit chow diet, Palm Springs, liver tissue

organism: Neotoma bryanti

value: Palm Springs


title: ATN-1 control

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

description: control

hyb_protocol: As materials and methods for CodeLinkTM Bioarray (Filgen).

scan_protocol: GenePix® 4400A (Molecular Devices, Inc)

data_processing: Microarray Data Analysis Tool Ver3.2 (Filgen).

organism: Homo sapiens

source_name: ATL cell line

label_protocol: Codelink

growth_protocol: Cells were cultured in Arteimis-1 medium with and without 2% Human serum. Artemis-1 is chemically defined, serum-free medium purchased from NihonTechno Service Co. Ltd. (Ibaraki, Japan).

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: To transfect miR-150 into cell lines, we used pLenti6/EmGFP-premicro-RNA.

tag: cell line

tag: cell type

value: ATL cell line

tag: transfection

value: control


title: C.elegans hydrogen sulfide sample replicate 3

source_name: C.elegans hydrogen sulfide exposure, replicate 3

tag: treatment

value: hydrogen sulfide exposure


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_wild-type_sample6

description: This RNA sample was collected from male strobili of a wild-type individual no. 41 derived from Toyama 1 half-sib F2 pedigree on September 19th, 2007. It is the sixth of seven fertile male strobilus samples with pre-meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 41

value: Wild-type

value: normal


title: ATN-1 miR-150

description: test

value: miR-150 transfection


title: 307_N.bryanti_control_PS

description: AID 307, Neotoma bryanti, control rabbit chow diet, Palm Springs, liver tissue


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_wild-type_sample5

description: This RNA sample was collected from male strobili of a wild-type individual no. 37 derived from Toyama 1 half-sib F2 pedigree on September 19th, 2007. It is the fifth of seven fertile male strobilus samples with pre-meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 37


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_wild-type_sample7

description: This RNA sample was collected from male strobili of a wild-type individual no. 42 derived from Toyama 1 half-sib F2 pedigree on September 19th, 2007. It is the seventh of seven fertile male strobilus samples with pre-meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 42


title: HH control

description: control

source_name: CTCL cell line

value: HH

value: CTCL cell line


title: 304_N.bryanti_control_PS

description: AID 304, Neotoma bryanti, control rabbit chow diet, Palm Springs, liver tissue


title: 305_N.bryanti_control_PS

description: AID 305, Neotoma bryanti, control rabbit chow diet, Palm Springs, liver tissue


title: HH miR-150

description: test


title: 217_N.bryanti_control_CW

description: AID 217, Neotoma bryanti, control rabbit chow diet, Caspers Wilderness, liver tissue

value: Caspers Wilderness


title: My-La control

description: control

value: My-La


title: 216_N.bryanti_control_CW

description: AID 216, Neotoma bryanti, control rabbit chow diet, Caspers Wilderness, liver tissue


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_wild-type_sample1

description: This RNA sample was collected from male strobili of a wild-type individual no. 22 derived from Toyama 1 half-sib F2 pedigree on September 18th, 2005. It is the first of seven fertile male strobilus samples with pre-meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 22

value: male strobili with pre-meiotic stage of pollen development


title: 10M [aCGH]

type: genomic

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

hyb_protocol: Equimolar mixture of labeled normal and tumor DNA was applied to the Agilent Human Genome CGH 2x400k Microarray.  Hybridization was carried out at 65°C for 40 hours, in a rotating oven at 20 rpm.

scan_protocol: CGH-v4_95. Feature extraction v.9.5

data_processing: The data quality of each microarray was assessed using the Quality Metrics report generated by the Agilent CGH analytics software (v.3.4).  Copy number aberrations were detected using the Aberration Detection Method (ADM-1) algorithm, based on computing significance scores for all genomic intervals. Before calling any aberration the log ratios are normalized  by subtracting the expected average µ from all log ratios vi, and then these modified log ratios are divided by the estimated variance σ. This transforms the log ratio scores into a normal distribution with a mean of 0 under the null model assumption.

molecule: genomic DNA

label_protocol: The Genomic DNA ULS labeling kit for FFPE Samples (Agilent) was used to chemically label 1 mg of genomic DNA with either ULS-Cy5 (tumor) or ULS-Cy3 dye (normal/reference DNA) according to the manufacturer’s protocol (Agilent Technologies, Inc., Palo Alto, CA).

growth_protocol: not applicable

extract_protocol: Genomic DNA was extracted from the tumor samples using QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).

treatment_protocol: 1M, 2M, 4M, 9M, 12M received chemo while 10M received radiation.

value: metastatic tumor

value: radiation

source_name: normal female - control/ reference DNA

value: blood

tag: sample type

value: normal female reference DNA (control)


title: 13P [aCGH]

value: primary tumor


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_wild-type_sample3

description: This RNA sample was collected from male strobili of a wild-type individual no. 973 derived from Toyama 1 half-sib F2 pedigree on September 22th, 2006. It is the third of seven fertile male strobilus samples with pre-meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 973


title: 10P [aCGH]


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_wild-type_sample2

description: This RNA sample was collected from male strobili of a wild-type individual no. 30 derived from Toyama 1 half-sib F2 pedigree on September 26th, 2006. It is the second of seven fertile male strobilus samples with pre-meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 30


title: 14P [aCGH]

source_name: tumor_primary (recurrence)

value: primary (recurrence) tumor


title: HUT78 control

description: control


title: 214_N.bryanti_control_CW

description: AID 214, Neotoma bryanti, control rabbit chow diet, Caspers Wilderness, liver tissue

value: male

value: control: rabbit chow

value: liver


title: 206_N.bryanti_control_CW

description: AID 206, Neotoma bryanti, control rabbit chow diet, Caspers Wilderness, liver tissue

value: female


title: alcohol-3

status: Public on Jul 29 2013

city: Beijing

first: Ji-lai

last: Liu

state: Beijing

address: Taiping road 27

department: Biochemistry and Molecular Biology

country: China

institute: Beijing Institute of Radiation Medicine

description:
This sample is the mix of cerebellar tissues from three drunk rats. It is the third of three replicates used in the experimental groups.
Sample 3

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package.

organism: Rattus norvegicus

source_name: cerebellum from drunk rats

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
All rats weighing approximately 240-260 g were kept under constant conditions (ambient temperature 22 °C and 55% humidity) for one week, and were ensured free access to food and 12-hour light/dark cycle. All animal feeding and care were performed in accordance with experimental animal feeding legislations mandated by National Science Council of People’s Republic of China.
After 12-hour fasting, experimental rats (9 per group) were fed by gavage with 40% alcohol (15ml/kg) while control rats (9 per group) were fed with the same amount of saline.

extract_protocol: RNA Extract Kit (Invitrogen) was used to extract total RNA. RNA quantity was determined with the NanoDrop ND-1000. RNA integrity was tested using standard denaturing agarose gel electrophoresis.

value: Sprague-Dawley

value: gavage with 40% alcohol (15ml/kg)

tag: weight

value: cerebellum


title: 12M [aCGH]

value: chemo


title: 11P [aCGH]


title: My-La miR-150

description: test

value: CTCL cell line

value: miR-150 transfection


title: HUT78 miR-150

description: test


title: alcohol-2

description:
This sample is the mix of cerebellar tissues from three drunk rats. It is the second of three replicates used in the experimental groups.
Sample 2


title: alcohol-1

description:
This sample is the mix of cerebellar tissues from three drunk rats. It is the first of three replicates used in the experimental groups.
Sample 1


title: brine-3

description:
This sample is the mix of cerebellar tissues from three control rats. It is the third of three replicates used in the control groups
Sample 6

source_name: cerebellum from control rats

value: gavage with brine (15ml/kg)


title: brine-1

description:
This sample is the mix of cerebellar tissues from three control rats. It is the first of three replicates used in the control groups
Sample 4


title: Cryptomeria_japonica_male_strobili_pollen_development_PM_wild-type_sample4

description: This RNA sample was collected from male strobili of a wild-type individual no. 31 derived from Toyama 1 half-sib F2 pedigree on September 19th, 2007. It is the fourth of seven fertile male strobilus samples with pre-meiotic stage of pollen development.

source_name: Cryptomeria japonica wild-type 31

value: Wild-type

value: normal

value: male strobili with pre-meiotic stage of pollen development


title: 9M [aCGH]

value: metastatic tumor

value: blood

value: normal female reference DNA (control)


title: 6M [aCGH]


title: 8M [aCGH]


title: 7P [aCGH]

value: primary tumor


title: WT seedlings vs paps1-1 seedlings_4

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

hyb_protocol: Labelling and array hybridization were carried out by CRX Biosciences Ltd (Dundee, UK).

scan_protocol: Scanned on Agilent Technologies Scanner G2505C US10350382. Quantification using Agilent Feature Extraction 10.7.3.1.

data_processing: Data were analyzed using R/Bioconductor, microarrays were normalized using the loess method of the Limma package.

organism: Arabidopsis thaliana

source_name: WT seedlings

growth_protocol: All plants were grown at 21°C. For inflorescence collection, main inflorescences excluding the open flowers/buds were collected from 30 day-old plants grown on soil. Whole seedlings including roots were harvested from 11 day old (mutant) or 9 day old (WT) plants grown on MS plates. The different ages were used to ensure that the first true leaves were at a comparable developmental stage. Plants were grown in long day conditions, and material was collected at 5 to 7 hours after the light period starts.

extract_protocol: Total RNA was prepared by the hot phenol method and cleaned up with QIAGEN RNAeasy Kit, digested with TURBO Dnase (Ambion).

value: WT

value: whole seedling

tag: ecotype

value: Ler

source_name: paps1-1 seedlings


title: 4M [aCGH]


title: 1M [aCGH]


title: paps1-1 seedlings vs WT seedlings_1

label_protocol: Labelling and array hybridization were carried out by CRX Biosciences Ltd (Dundee, UK).


title: 2M [aCGH]


title: paps1-1 inflorescences vs WT inflorescences_2

source_name: paps1-1 inflorescences

value: inflorescences

source_name: WT inflorescences


title: WT inflorescences vs paps1-1 inflorescences_4


title: paps1-1 seedlings vs WT seedlings_2


title: Adult control frontal lobe [AC7]

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

institute: Barts & The London School of Medicine & Dentistry

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in GenomeStudio

source_name: Adult control frontal lobe AC7  (BioChain #A803160)

label_protocol: Cy3 Standard illumina prorocol

extract_protocol: RNA was extracted with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: Adult control frontal lobe

tag: Sex

value: M


title: WT inflorescences vs paps1-1 inflorescences_3


title: Adult control frontal lobe [AC5]

source_name: Adult control frontal lobe AC5  (BioChain #B210079)

tag: age


title: heart_control_rep4

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: replicate 4

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

organism: Mus musculus

source_name: 25 weeks, young control

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

treatment_protocol: Male C57BL6/J Rj mice were obtained from Janvier (France) and were randomly assigned to rapamycin or vehicle treatment groups. We had three treatment cohorts, distinguished by age of treatment onset. Treatment was initiated in young adulthood (i.e., at approx. 4 months of age), in midlife (i.e., at 13 months of age) or late in life (i.e., at 20-22 months of age). Animals were treated for >12 months before analyses started at 16 months, 25 months and 34 months of age, respectively. Animals were kept on their respective diet for the entirety of the study. In all cases, the experimenter was blinded to the animal group assignments.

tag: tissue

value: heart

value: wildtype

value: 25 weeks

tag: mouse id


title: heart_control_rep3

description: replicate 3

tag: strain

tag: genotype


title: paps1-1 inflorescences vs WT inflorescences_1


title: heart_treated_rep4

description: replicate 4

source_name: 25 month, rapamycin treated

value: 25 month


title: WT seedlings vs paps1-1 seedlings_3


title: heart_treated_rep2

description: replicate 2


title: Gametophyte sample 5 (Cy3) vs. Mid-sporophyte sample 2 (Cy5)

city: Sheffield

first: Martin-Timothy

last: O'Donoghue

address: Western Bank

department: Department of Animal and Plant Sciences

institute: University of Sheffield

hyb_protocol: Samples were hybridized to microarrays by MOgene LC, an Agilent certified facility based in St Louis, MO, USA (www.mogene.com, MOGene LC, St. Louis following Agilent protocols.

scan_protocol: Microarrays were scanned by MOgene LC.

data_processing: Image processing was carried out by MOgebe LC.

organism: Physcomitrium patens

source_name: Gametophytic protonemal tissue of Physcomitrella patens sample 5

label_protocol: Samples were co-hybridised as total RNA with Cyanine (Cy-3) fluorescent ULS labels MOgene LC, an Agilent certified facility based in St Louis, MO, USA (www.mogene.com, MOGene LC, St. Louis)

extract_protocol: RNA was extracted from all plant tissues using the Spectrum Total Plant RNA extraction kit (Sigma, STRN250) following manufacturer’s recommendations. Approximately 100mg of tissue was harvested directly into liquid nitrogen in microcentrifuge tubes and ground to a powder. RNA integrity and concentration were analysed by agarose gel electrophoresis and an Agilent Bioanalyzer. Gametophyte RNA was extracted from seven day old protomenal tissue.

treatment_protocol: No treatment was used

value: Villesexel

value: 7 day old protonemal tissue

source_name: Mid-sporophytic tissue of Physcomitrella patens sample 2

label_protocol: Samples were co-hybridised as total RNA with Cyanine (Cy-5) fluorescent ULS labels MOgene LC, an Agilent certified facility based in St Louis, MO, USA (www.mogene.com, MOGene LC, St. Louis)

growth_protocol: Plants were grown in Sanyo MLR incubators with a 16-hour photoperiod (140 µmol m 2), 22°C day temperature and 16°C night temperature. Protonema and gametophores were grown on organic-nitrogen-supplemented BCD medium in sterile petri dishes overlaid with sterile cellophane discs and sealed with micropore tape, as described (Knight et al, 2002). Gametophore production was initiated by sub-culturing protonemal fragments onto agar lacking cellophane discs and culturing these for longer than 14 days. Gametogenesis was initiated by transferring cultures to 15°C growth cabinet for three weeks with a 16-hour photoperiod (140 µmol m 2), after which they were flooded with sterile deionised water to promote fertilization of archegonia for about 2 hours. Subsequently the cultures were returned to gametophyte growth conditions for further development of the sporophytes.

value: Mid-sporophytic tissue (defined as ovoid to near-spherical translucent green capsules with the foot, calyptras and calyptral remnants removed)


title: heart_treated_rep3

description: replicate 3


title: Adult control frontal lobe [AC2]

source_name: Adult control frontal lobe AC2  (BioChain #A803159)


title: Dye swap Early sporophyte sample 3 (Cy3) vs. Gametophyte sample 3 (Cy5)

source_name: Early sporophytic tissue of Physcomitrella patens sample 3

treatment_protocol: Gametogenesis was initiated by transferring cultures to 15°C growth cabinet for three weeks with a 16-hour photoperiod (140 µmol m 2), after which they were flooded with sterile deionised water to promote fertilization of archegonia for about 2 hours. Subsequently the cultures were returned to gametophyte growth conditions for further development of the sporophytes.

value: Early sporophytic tissue (defined as as pre-expanded columnar capsules with the foot, calyptras and calyptral remnants removed)

source_name: Gametophytic protonemal tissue of Physcomitrella patens sample 3

growth_protocol: Plants were grown in Sanyo MLR incubators with a 16-hour photoperiod (140 µmol m 2), 22°C day temperature and 16°C night temperature. Protonema and gametophores were grown on organic-nitrogen-supplemented BCD medium in sterile petri dishes overlaid with sterile cellophane discs and sealed with micropore tape, as described (Knight et al, 2002).

extract_protocol: RNA was extracted from all plant tissues using the Spectrum Total Plant RNA extraction kit (Sigma, STRN250) following manufacturer’s recommendations. Approximately 100mg of tissue was harvested directly into liquid nitrogen in microcentrifuge tubes and ground to a powder. RNA integrity and concentration were analysed by agarose gel electrophoresis and an Agilent Bioanalyzer.


title: Gametophyte sample 3 (Cy3) vs. Early sporophyte sample 3 (Cy5)


title: heart_control_rep1

description: replicate 1


title: Gametophyte sample 2 (Cy3) vs Early sporophyte sample 2 (Cy5)

source_name: Gametophytic protonemal tissue of Physcomitrella patens sample 2

extract_protocol: RNA was extracted from all plant tissues using the Spectrum Total Plant RNA extraction kit (Sigma, STRN250) following manufacturer’s recommendations. Approximately 100mg of tissue was harvested directly into liquid nitrogen in microcentrifuge tubes and ground to a powder. RNA integrity  and  concentration  were  analysed  by  agarose  gel  electrophoresis  and  an  Agilent Bioanalyzer. Gametophyte RNA was extracted from seven day old protomenal tissue.

value: 7 day old protomenal tissue

source_name: Early sporophytic tissue of Physcomitrella patens sample 2

growth_protocol: Plants were grown in Sanyo MLR incubators with a 16-hour photoperiod (140 µmol m  2), 22°C day temperature and 16°C night temperature. Protonema and gametophores were grown on organic-nitrogen-supplemented BCD medium in sterile petri dishes overlaid with sterile cellophane discs and sealed with micropore tape, as described (Knight et al, 2002). Gametophore production was initiated by sub-culturing protonemal fragments onto agar lacking cellophane discs and culturing these for longer than 14 days. Gametogenesis was initiated by transferring cultures to 15°C growth cabinet for three weeks with a 16-hour photoperiod (140 µmol m  2), after which they were flooded with sterile deionised water to promote fertilization of archegonia for about 2 hours. Subsequently the cultures were returned to gametophyte growth conditions for further development of the sporophytes.


title: Adult control frontal lobe [AC6]

source_name: Adult control frontal lobe AC6  (BioChain #A507293)


title: Gametophyte sample 4 (Cy3) vs. Mid-sporophyte sample 1 (Cy5)

source_name: Gametophytic protonemal tissue of Physcomitrella patens sample 4

source_name: Mid-sporophytic tissue of Physcomitrella patens sample 1


title: Foetal Frontal Lobe [FC8]

source_name: Foetal Frontal Lobe FC8  (BioChain #B207215)

value: Foetal Frontal Lobe

value: 38 weeks


title: heart_treated_rep1

description: replicate 1


title: heart_y control_rep2

description: replicate 2

source_name: 25 month, control


title: Dye swap Mid-sporophyte sample 3 (Cy3) vs.Gametophyte sample 6 (Cy5)

source_name: Mid-sporophytic tissue of Physcomitrella patens sample 3

source_name: Gametophytic protonemal tissue of Physcomitrella patens sample 6


title: Gametophyte sample 1 (Cy3) vs. Early sporophyte sample 1 (Cy5)

source_name: Gametophytic protonemal tissue of Physcomitrella patens sample 1

growth_protocol: Plants were grown in Sanyo MLR incubators with a 16-hour photoperiod (140 µmol m  2), 22°C day temperature and 16°C night temperature. Protonema and gametophores were grown on organic-nitrogen-supplemented BCD medium in sterile petri dishes overlaid with sterile cellophane discs and sealed with micropore tape, as described (Knight et al, 2002).

source_name: Early sporophytic tissue of Physcomitrella patens sample 1

extract_protocol: RNA was extracted from all plant tissues using the Spectrum Total Plant RNA extraction kit (Sigma, STRN250) following manufacturer’s recommendations. Approximately 100mg of tissue was harvested directly into liquid nitrogen in microcentrifuge tubes and ground to a powder. RNA integrity  and  concentration  were  analysed  by  agarose  gel  electrophoresis  and  an  Agilent Bioanalyzer.

treatment_protocol: Gametogenesis was initiated by transferring cultures to 15°C growth cabinet for three weeks with a 16-hour photoperiod (140 µmol m  2), after which they were flooded with sterile deionised water to promote fertilization of archegonia for about 2 hours. Subsequently the cultures were returned to gametophyte growth conditions for further development of the sporophytes.


title: Gametophyte sample 6 (Cy3) vs. Mid-sporophyte sample 3 (Cy5)


title: brine-2

description:
This sample is the mix of cerebellar tissues from three control rats. It is the second of three replicates used in the control groups
Sample 5

source_name: cerebellum from control rats

value: Sprague-Dawley

value: gavage with brine (15ml/kg)

value: male

value: cerebellum


title: Foetal Frontal Lobe [FC6]

source_name: Foetal Frontal Lobe FC6  (BioChain #B111144)

value: F

value: 32 weeks


title: heart_control_rep2

description: replicate 2

source_name: 25 weeks, young control

value: heart


title: Foetal Frontal Lobe [FC7]

source_name: Foetal Frontal Lobe FC7  (BioChain #B207216)

value: 20 weeks


title: 7M_2 [aCGH]

value: metastatic tumor

source_name: normal female - control/ reference DNA

value: blood

value: normal female reference DNA (control)


title: Foetal Frontal Lobe [FC5]

source_name: Foetal Frontal Lobe FC5  (BioChain #B205045)

value: M


title: 7M_1 [aCGH]


title: brain_treated_rep3

description: replicate 3

source_name: 25 month, rapamycin treated

value: brain

value: wildtype

value: 25 month


title: brain_control_rep4

description: replicate 4

value: 25 weeks


title: Foetal Cerebellum [FC3]

source_name: Foetal Cerebellum FC3  (BioChain #B211067)

value: Foetal Cerebellum

value: 24 weeks


title: brain_treated_rep4

description: replicate 4


title: brain_control_rep3

description: replicate 3


title: brain_y control_rep2

description: replicate 2


title: brain_control_rep2

description: replicate 2


title: Foetal Cerebellum [FC4]

source_name: Foetal Cerebellum FC4  (BioChain #B304024)

value: 26 weeks


title: Foetal Cerebellum [FC1]

source_name: Foetal Cerebellum FC1 (BioChain #B205044)

value: 37 weeks


title: Foetal Cerebellum [FC2]

source_name: Foetal Cerebellum FC2  (BioChain #A602126)

value: 33 weeks


title: Choroid plexus papilloma [P2]

source_name: Paediartric brain tumour P2

value: Choroid plexus papilloma

tag: grade

value: I


title: Choroid plexus papilloma [P1]

source_name: Paediartric brain tumour P1

value: 10 months


title: Atypical teratoid/rhabdoid tumour [R4]

source_name: Paediartric brain tumour R4

value: Atypical teratoid/rhabdoid tumour

value: IV

value: 9 months


title: Choroid plexus papilloma [P3]

source_name: Paediartric brain tumour P4

value: F

value: nd


title: brain_control_rep1

description: replicate 1

value: brain


title: brain_treated_rep1

description: replicate 1

value: wildtype


title: Atypical teratoid/rhabdoid tumour [R3]

source_name: Paediartric brain tumour R3


title: heart_y control_rep1

description: replicate 1

source_name: 25 month, control

value: heart

value: 25 month


title: kidney_treated_rep4

description: replicate 4

value: kidney


title: kidney_treated_rep2

description: replicate 2


title: kidney_control_rep4

description: replicate 4

value: 25 weeks


title: brain_y control_rep1

description: replicate 1


title: Medulloblastoma [M9]

source_name: Paediartric brain tumour M9

value: Medulloblastoma

value: M


title: Atypical teratoid/rhabdoid tumour [R5]

source_name: Paediartric brain tumour R5

value: 2 months


title: kidney_treated_rep3

description: replicate 3


title: Atypical teratoid/rhabdoid tumour [R2]

source_name: Paediartric brain tumour R2

value: 7 months


title: kidney_control_rep1

description: replicate 1

source_name: 25 weeks, young control


title: kidney_control_rep2

description: replicate 2


title: Atypical teratoid/rhabdoid tumour [R1]

source_name: Paediartric brain tumour R1


title: kidney_control_rep3

description: replicate 3


title: P14 retina 1 WT Cbp allele rep2

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description:
P14_Retina_3_2
7530 - 3-2 (RM-1452_plus_1458)

hyb_protocol: 1.5 ug of each aRNA sample was applied to MouseWG-6 v2 Expression BeadChips and hybridized at 58C for 16-20 hours at high humidity, and immobilized, biotinylated aRNAs were then detected by staining with cy3 Steptavidin for 10 minutes at room temperature. Arrays were washed and dried according to Illumina standard protocol.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader, laser power and PMT voltage were kept constant for Cy3 scans, and then images were quantitated by Illumina Beadscan (v3).

data_processing: Quantitated data were processed in GenomeStudio (v.2011) to generate signal intensity for each probe sets, and exported as non-normalized, background retained set and quantile-normalized, background subtracted set of data.

source_name: P14 retina WT Cbp allele

label_protocol: Samples are standardly prepared and labeled with dye cy3 using LifeTechnologies Illumina-TotalPrep kits.

growth_protocol: Retinas were extracted from P14 mouse pups. Mothers were fed Purina Mouse Chow ad lib.

extract_protocol: Total RNA was extracted using Qiagen RNEasy kit, quantified and quality-checked using Nanodrop, then sent to WUSM GTAC genomics core for quality assessment using Agilent Technologies 2100 Bioanalyzer “Lab-on-a-chip” system.  Equal amounts of high-quality (RIN score >8.0) RNA samples from one male and one female littermate were pooled for microarray assay.

treatment_protocol: Retinas were dissected in late afternoon and placed in Qiagen RNAlater medium until extraction.

tag: strain background

tag: genotype/variation

value: Rho-iCre+; Cbp +/Fl; p300 Fl/Fl

value: male and female pooled

value: Retina


title: Medulloblastoma [M7]

source_name: Paediartric brain tumour M7

value: IV


title: Medulloblastoma [M5]

source_name: Paediartric brain tumour M5


title: kidney_y control_rep2

description: replicate 2


title: Medulloblastoma [M3]

source_name: Paediartric brain tumour M3

value: 6 months


title: Medulloblastoma [M8]

source_name: Paediartric brain tumour M8


title: P14 Retina Rho-iCre+ rep1

description:
P14_Retina_2_1
7526 - 2-1 (RP-530_plus_533)

source_name: P14 Retina Rho-iCre+

value: Rho-iCre+; Cbp WT; p300 WT

tag: gender


title: Medulloblastoma [M6]

source_name: Paediartric brain tumour M6


title: kidney_y control_rep1

description: replicate 1


title: Medulloblastoma [M4]

source_name: Paediartric brain tumour M4


title: P14 Retina Cbp&p300 CKO rep2

description:
P14_Retina_5_2
7521 - 5-2 (RM-1287_plus_1303)

source_name: P14 Retina Cbp&p300 CKO

value: Rho-iCre+; Cbp Fl/Fl; p300 Fl/Fl


title: kidney_treated_rep1

description: replicate 1

source_name: 25 month, rapamycin treated


title: P14 Retina Cbp CKO rep2

description:
P14_Retina_6_2a
7538 - 6-2a (RC-211)

source_name: P14 Retina Cbp CKO

value: Rho-iCre+; Cbp Fl/Fl; p300 WT/WT


title: P14 Retina p300 CKO rep2

description:
P14_Retina_7_2a
7541 - 7-2a (RP-582)

source_name: P14 Retina p300 CKO

value: Rho-iCre+; Cbp WT/WT; p300 Fl/Fl


title: P14 Retina C57Bl/6 rep2

description:
P14_Retina_8_2
7535 - 8-2 (C57BI/6 _number_2)

source_name: P14 Retina C57Bl/6

value: wild type


title: P14 retina 1 WT p300 allele rep3

description:
P14_Retina_4_2a
7536 - 4-2a

source_name: P14 retina WT p300 allele

value: Rho-iCre+; Cbp Fl/Fl; p300 +/Fl


title: Grafted sphere-induced tumour, Pten/Rb background, PRCATR11

first: Nick

last: Henriquez

address: 29 Gordon Square

department: Enterprise

institute: UCL

description:
PRCATR11
Dissected brain-derived tumour tissue.

hyb_protocol: Standard Affymetrix hybridisation protocol.

scan_protocol: Standard Affymetrix scanning protocol using the GeneChip Scanner 3000 7G.

data_processing:
Data were imported into Partek using RMA background correction and quantile normalisation with GC-correction. Core exons were used in the analysis. Transcript assignments are based on genome build mm8.
Probe group file: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Grafted sphere-induced tumour

label_protocol: Standard Affymetrix labelling protocol.

extract_protocol: Samples from neurospheres of defined genotypes and from mice injected with transformed spheres/AdCre that showed signs of tumour burden were snap-frozen and lysed with Trizol, following which RNA was extracted and used for subsequent microarray hybridisation.

tag: genetic background

value: mixed (intercrossed C57, FVB, and mainly 129 Ola)

value: Pten/Rb Flox-Hom

value: brain-derived tumor tissue

tag: tumour type

value: GC-GBM

tag: derivation

value: in vitro AdCre-transduced, grafted spheres


title: Grafted sphere-induced tumour, Pten/Rb background, PRCATR12

description:
PRCATR12
Dissected brain-derived tumour tissue.


title: Grafted sphere-induced tumour, Pten/Rb background, PRCATR10

description:
PRCATR10
Dissected brain-derived tumour tissue.


title: P14 retina 1 WT p300 allele rep1

description:
P14_Retina_4_1
7532 - 4-1 (RM-1357_plus_1365)


title: Ependymoma [E13]

source_name: Paediartric brain tumour E13

value: Ependymoma

value: II

value: F


title: P14 Retina Rho-iCre+ rep3

description:
P14_Retina_2_3a
7528 - 2-3a (RP-553)

value: male and female pooled

value: Retina


title: Medulloblastoma [M1]

source_name: Paediartric brain tumour M1

value: Medulloblastoma

value: IV

value: M


title: P14 Retina Cre neg rep2

description:
P14_Retina_1_2
7524 - 1-2 (RM-1293_plus_1300)

source_name: P14 Retina Cre neg

value: Cre neg; Cbp Fl/Fl; p300 Fl/Fl


title: Ependymoma [E14]

source_name: Paediartric brain tumour E14

value: III


title: AdGFP-tranduced neurospheres (p3) p53/Pten background, GFP5P1

description:
GFP5P1
Pelleted spheres from neurosphere culture (p3 after AdGFP).

source_name: AdGFP-tranduced neurospheres

value: p53/Pten Flox-Hom

tag: cell type

value: neurospheres

value: in vitro AdGFP-transduced, cultured spheres


title: AdGFP-tranduced neurospheres (p3) Pten/Rb background, GFPPR1

description:
GFPPR1
Pelleted spheres from neurosphere culture (p3 after AdGFP).

value: mixed (intercrossed C57, FVB, and mainly 129 Ola)

value: Pten/Rb Flox-Hom


title: AdGFP-tranduced neurospheres (p3) p53/Rb background, GFP5R1

description:
GFP5R1
Pelleted spheres from neurosphere culture (p3 after AdGFP).

value: p53/Rb Flox-Hom


title: Ependymoma [E12]

source_name: Paediartric brain tumour E12


title: AdCre-transformed neurosphere (p3) Pten/Rb background, CSPR1

description:
CSPR1
Pelleted spheres from neurosphere culture (p3 after AdCre).

source_name: AdCre-transformed neurosphere

value: in vitro AdCre-transduced, cultured spheres


title: P14 Retina Cre neg rep3

description:
P14_Retina_1_3a
7525 - 1-3a (RM-1412) 1-3b (RM-1430)


title: Medulloblastoma [M2]

source_name: Paediartric brain tumour M2


title: P14 Retina Cbp&p300 CKO rep3

description:
P14_Retina_5_3
7522 - 5-3 (RM-1294_plus_1299)

value: Rho-iCre+; Cbp Fl/Fl; p300 Fl/Fl


title: P14 Retina p300 CKO rep3

description:
P14_Retina_7_3a
7542 - 7-3a (RM-1626)

value: Rho-iCre+; Cbp WT/WT; p300 Fl/Fl


title: P14 Retina Cbp CKO rep1

description:
P14_Retina_6_1a
7537 - 6-1a (RC-210)

value: Rho-iCre+; Cbp Fl/Fl; p300 WT/WT


title: P14 Retina C57Bl/6 rep3

description:
P14_Retina_8_3
7543 - 8-3 (C57Bl/6 MplusF)

value: wild type

value: male and female pooled


title: Ependymoma [E8]

source_name: Paediartric brain tumour E8

value: Ependymoma

value: II


title: P14 retina 1 WT Cbp allele rep3

description:
P14_Retina_3_3
7531 - 3-3 (RM-1455_plus_1459)

source_name: P14 retina WT Cbp allele

value: Rho-iCre+; Cbp +/Fl; p300 Fl/Fl

value: Retina


title: AdCre-transformed neurosphere (p3) p53/Rb background, CS5R2

description:
CS5R2
Pelleted spheres from neurosphere culture (p3 after AdCre).


title: Ependymoma [E9]

source_name: Paediartric brain tumour E9

value: M


title: AdCre-transformed neurosphere (p3) Pten/Rb background, CSPR2

description:
CSPR2
Pelleted spheres from neurosphere culture (p3 after AdCre).


title: AdCre-transformed neurosphere (p3) p53/Rb background, CS5R1

description:
CS5R1
Pelleted spheres from neurosphere culture (p3 after AdCre).


title: Ependymoma [E10]

source_name: Paediartric brain tumour E10


title: P14 Retina Cbp CKO rep3

description:
P14_Retina_6_3a
7539 - 6-3a (RC-235)

source_name: P14 Retina Cbp CKO


title: AdCre-transformed neurosphere (p3) p53/Pten background, CS5P1

description:
CS5P1
Pelleted spheres from neurosphere culture (p3 after AdCre).

value: p53/Pten Flox-Hom


title: brain_treated_rep2

description: replicate 2

source_name: 25 month, rapamycin treated

value: brain

value: wildtype

value: 25 month


title: AdCre-transformed neurosphere (p3) p53/Pten/Rb background, CS3x2

description:
CS3x2
Pelleted spheres from neurosphere culture (p3 after AdCre).

value: mixed (intercrossed C57, FVB, and mainly 129 Ola)

value: p53/Pten/Rb Flox-Hom

value: neurospheres


title: P14 retina 1 WT p300 allele rep2

description:
P14_Retina_4_2
7533 - 4-2 (RM-1423_plus_1426)

value: Rho-iCre+; Cbp Fl/Fl; p300 +/Fl


title: P14 Retina C57Bl/6 rep1

description:
P14_Retina_8_1
7534 - 8-1 (C57BI/6 _number_1)

source_name: P14 Retina C57Bl/6


title: AdCre-transformed neurosphere (p3) p53/Pten background, CS5P2

description:
CS5P2
Pelleted spheres from neurosphere culture (p3 after AdCre).

value: in vitro AdCre-transduced, cultured spheres


title: Ependymoma [E5]

source_name: Paediartric brain tumour E5


title: P14 Retina Rho-iCre+ rep2

description:
P14_Retina_2_2a
7527 - 2-2a (RP-552)

source_name: P14 Retina Rho-iCre+

value: Rho-iCre+; Cbp WT; p300 WT


title: AdCre-transformed neurosphere (p3) p53/Pten/Rb background, CS3x1

description:
CS3x1
Pelleted spheres from neurosphere culture (p3 after AdCre).


title: P14 Retina Cre neg rep1

description:
P14_Retina_1_1
7523 - 1-1 (RM-1237_plus_1251)

value: Cre neg; Cbp Fl/Fl; p300 Fl/Fl


title: Grafted sphere-induced tumour, p53/Rb background, 5RCATR5

description:
5RCATR5
Dissected brain-derived tumour tissue.

source_name: Grafted sphere-induced tumour

value: p53/Rb Flox-Hom

value: brain-derived tumor tissue

value: oligo-astrocytoma

value: in vitro AdCre-transduced, grafted spheres


title: P14 Retina p300 CKO rep1

description:
P14_Retina_7_1a
7540 - 7-1a (RP-575)

source_name: P14 Retina p300 CKO

value: Rho-iCre+; Cbp WT/WT; p300 Fl/Fl

value: male and female pooled

value: Retina


title: Grafted sphere-induced tumour, p53/Rb background, 5RCATR6

description:
5RCATR6
Dissected brain-derived tumour tissue.


title: Choroid plexus papilloma [P4]

source_name: Paediartric brain tumour P3

value: Choroid plexus papilloma

value: I

value: M


title: P14 Retina Cbp&p300 CKO rep1

description:
P14_Retina_5_1
7520 - 5-1 (RM-1233_plus_1235)

source_name: P14 Retina Cbp&p300 CKO

value: Rho-iCre+; Cbp Fl/Fl; p300 Fl/Fl


title: Ependymoma [E2]

source_name: Paediartric brain tumour E2

value: Ependymoma

value: III

value: F


title: Ependymoma [E1]

source_name: Paediartric brain tumour E1


title: AdCre-induced tumour, p53/Rb background, 5RCA44

description:
5RCA44
Dissected brain-derived tumour tissue.

source_name: AdCre-induced tumour

value: mixed (intercrossed C57, FVB, and mainly 129 Ola)

value: intra-cranioventricular AdCre


title: Grafted sphere-induced tumour, p53/Rb background, 5RCATR4

description:
5RCATR4
Dissected brain-derived tumour tissue.


title: P14 retina 1 WT Cbp allele rep1

description:
P14_Retina_3_1a
7529 - 3-1a (RM-1451) 3-1b (RM-1457)

value: Rho-iCre+; Cbp +/Fl; p300 Fl/Fl


title: Glioblastoma [GBM5]

source_name: Paediartric brain tumour GBM5

value: Glioblastoma

value: IV


title: Glioblastoma [GBM4]

source_name: Paediartric brain tumour GBM4


title: Ependymoma [E11]

source_name: Paediartric brain tumour E11

value: ND

value: nd


title: Strain with ZNC1-GAL4AD fusion, wild type background, artificially activated ZNC1 - log phase - rep3

city: Würzburg

first: Rebecca

last: Schillig

address: Josef-Schneider-Straße 2 /Bau D15

institute: Institute for Molecular Infection Biology

description:
ZNC1-3
Log phase gene expression with the putative hyperactive zinc cluster transcription factor ZNC1.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to 25ul fragmentation mixture (50ul total) and hybridized to custom Agilent Candida albicans 15.7K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565-CA) using one color scan setting for 8x15k array slides Scan Area 61 x 21,6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 016356_D_F_20070525) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. VSN normalization was applied.

organism: Candida albicans

source_name: Strain with ZNC1-GAL4AD fusion

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labelling kit , one color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Overnight cultures were diluted 1:100 in fresh YPD media; growth to log phase: ca. 4h at 30°C, shaking.

extract_protocol: RNA isolation with hot phenol method combined with RNeasy Mini Kit Qiagen; storage of RNA at -80°C.

tag: background

tag: transcription factor activation


title: Ependymoma [E7]

source_name: Paediartric brain tumour E7


title: AdCre-induced tumour, p53/Rb background, 5RCA3

description:
5RCA3
Dissected brain-derived tumour tissue.

value: p53/Rb Flox-Hom

value: brain-derived tumor tissue

value: PNET


title: Strain with ZNC1-GAL4AD fusion, wild type background, artificially activated ZNC1 - log phase - rep2

description:
ZNC1-2
Log phase gene expression with the putative hyperactive zinc cluster transcription factor ZNC1.


title: Strain with ZNC1-GAL4AD fusion, wild type background, artificially activated ZNC1 - log phase - rep1

description:
ZNC1-1
Log phase gene expression with the putative hyperactive zinc cluster transcription factor ZNC1.


title: AdCre-induced tumour, p53/Rb background, 5RCA2

description:
5RCA2
Dissected brain-derived tumour tissue.


title: Glioblastoma [GBM3]

source_name: Paediartric brain tumour GBM3


title: Strain with ZCF34-GAL4AD fusion, wild type background, artificially activated ZCF34(MRR2) - log phase - rep2

description:
ZCF34-2
Log phase gene expression with the putative hyperactive zinc cluster transcription factor MRR2 (ZCF34).

source_name: Strain with ZCF34-GAL4AD fusion

value: MRR2 (ZCF34)


title: Glioblastoma [GBM1]

source_name: Paediartric brain tumour GBM1


title: Glioblastoma [GBM2]

source_name: Paediartric brain tumour GBM2


title: AdCre-induced tumour, p53/Rb background, 5RCA1

description:
5RCA1
Dissected brain-derived tumour tissue.


title: Grafted sphere-induced tumour, p53/Pten background, 5PCATR9

description:
5PCATR9
Dissected brain-derived tumour tissue.

value: p53/Pten Flox-Hom

value: oligo-astrocytoma

value: in vitro AdCre-transduced, grafted spheres


title: Strain with ZCF34-GAL4AD fusion, wild type background, artificially activated ZCF34(MRR2) - log phase - rep3

description:
ZCF34-3
Log phase gene expression with the putative hyperactive zinc cluster transcription factor MRR2 (ZCF34).


title: Grafted sphere-induced tumour, p53/Pten background, 5PCATR8

description:
5PCATR8
Dissected brain-derived tumour tissue.


title: Anaplastic astrocytoma [AA1]

source_name: Paediartric brain tumour AA1

value: Anaplastic astrocytoma

value: M


title: Anaplastic astrocytoma [AA2]

source_name: Paediartric brain tumour AA2

value: III

value: F


title: Strain with STB5-GAL4AD fusion, wild type background, artificially activated STB5 - log phase - rep3

description:
STB5-3
Log phase gene expression with the putative hyperactive zinc cluster transcription factor STB5.

source_name: Strain with STB5-GAL4AD fusion


title: Grafted sphere-induced tumour, p53/Pten background, 5PCATR6

description:
5PCATR6
Dissected brain-derived tumour tissue.

source_name: Grafted sphere-induced tumour

value: mixed (intercrossed C57, FVB, and mainly 129 Ola)


title: Ependymoma [E6]

source_name: Paediartric brain tumour E6

value: Ependymoma


title: Diffuse astrocytoma [DA3]

source_name: Paediartric brain tumour DA3

value: Diffuse astrocytoma

value: II


title: Diffuse astrocytoma [DA2]

source_name: Paediartric brain tumour DA2


title: Ependymoma [E3]

source_name: Paediartric brain tumour E3


title: Strain with ZCF34-GAL4AD fusion, wild type background, artificially activated ZCF34(MRR2) - log phase - rep1

description:
ZCF34-1
Log phase gene expression with the putative hyperactive zinc cluster transcription factor MRR2 (ZCF34).


title: Strain with STB5-GAL4AD fusion, wild type background, artificially activated STB5 - log phase - rep2

description:
STB5-2
Log phase gene expression with the putative hyperactive zinc cluster transcription factor STB5.


title: Strain with STB5-GAL4AD fusion, wild type background, artificially activated STB5 - log phase - rep1

description:
STB5-1
Log phase gene expression with the putative hyperactive zinc cluster transcription factor STB5.


title: AdCre-induced tumour, p53/Pten background, 5PCA3

description:
5PCA3
Dissected brain-derived tumour tissue.

source_name: AdCre-induced tumour

value: intra-cranioventricular AdCre


title: Thiosulfate_vs_RCV_III_csw

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 17 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).

data_processing: For background correction of spot intensities, ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Allochromatium vinosum DSM 180

source_name: RCV control

label_protocol: For synthesis of fluorescently-labeled cDNA with the fluorescent nucleotide analogues Cy3-dCTP and Cy5-dCTP (GE Healthcare, Freiburg, Germany) 25 μg of RNA and 500 ng of random hexamer primers were used. The reaction mixture (30 µl) contained 3 μl 1 mM Cy3-dCTP or Cy5-dCTP, 3 μl 0.1 M DTT, 6 μl 5x first strand buffer (Invitrogen, Karlsruhe, Germany), 0.6 μl dNTP-mix (25 mM each of dATP, dUTP, and dGTP and 10 mM dCTP) and 2 μl Superscript II reverse transcriptase (Invitrogen, Darmstadt, Germany). The mixture was incubated for 10 min at room temperature and 110 min at 42 °C, stopped by addition of 10 μl 0.1 N NaOH, incubated for 10 min at 70 °C, and then neutralized by addition of 10 μl 0.1 N HCl. cDNA samples were purified by washing three times with water on a Microcon column (Millipore, YM-30).

growth_protocol: Allochromatium vinosum DSM 180T wildtype cells were cultivated photolithoautotrophically in batch culture at 30°C under anaerobic conditions and continuous illumination in completely filled screw-capped culture bottles containing modified Pfennig´s medium (“0” medium without sulfide). Sulfide (4 mM), thiosulfate (10 mM), sulfite (5 mM) or sulfur (50 mM) were added to the cultures as sulfur sources. Cells of A. vinosum, grown photoorganoheterotrophically on malate (RCV medium) for three days were used as an inoculum for growth experiments. The culture volume of the precultures was 500 ml. Inoculum cells were harvested by centrifugation (10 min, 2680 x g) and washed once in “0” medium. For DNA microarray experiments cells were cultivated in a volume of 100 ml RCV or “0” medium supplemented with the respective sulfur source. These cultures were inoculated with stationary phase cells taken from 100 ml preculture.

extract_protocol: Total RNA of A. vinosum was isolated from cells grown photoorganoheterotrophically on 22 mM malate or photolithoautotrophically on 50 mM sulfur, 4 mM sulfide, 10 mM thiosulfate or 5 mM sulfite in 100 ml culture bottles. Briefly, cells of two culture aliquots (35 ml each) culture were harvested (12800 x g, 10 min, 4°C), each pellet was resuspended in 350 µl RLT buffer (Qiagen, Hilden, Germany) containing 10 mM DTT and disrupted by vortexing (Ivoclar Vivadent Silamat S 6, Ivoclar Vivadent AG, Schaan, Lichtenstein) using 0,1 mm Zirconia/Silica beads (Roth, Karlsruhe, Germany). Cell debris and glass beads were sedimented (15000 x g, 2 min, 4°C) and the supernatant was mixed with 500 µl phenol (1 min) followed by the addition of 500 µl chloroform and a further mixing step. After centrifugation (10000 x g, 10 min, 4°C) RNA of the supernatant was precipitated by the addition of 1/10 volume 3 M sodium acetate (pH 6) and two volumes of ice-cold ethanol. Precipitated RNA was collected by centrifugation (10000 x g, 10 min, 4°C) and the pellets generated from 70 ml culture were resuspended in 100 µl RNAse free water. The RNA was further purified using the RNAeasy Total RNA kit (Qiagen, Hilden, Germany) according to the manufactures instructions. RNA concentration was measured photometrically with an Analytic Jena Specord 210 spectrophotometer.

treatment_protocol: see growth protocol

tag: agent

value: RCV control

source_name: Thiosulfate

value: 10 mM Thiosulfate


title: AdCre-induced tumour, p53/Pten background, 5PCA1

description:
5PCA1
Dissected brain-derived tumour tissue.

value: brain-derived tumor tissue


title: Thiosulfate_vs_RCV_II


title: Strain with CTA4-GAL4AD fusion, wild type background, artificially activated CTA4 - log phase - rep3

description:
CTA4-3
Log phase gene expression with the putative hyperactive zinc cluster transcription factor CTA4.

source_name: Strain with CTA4-GAL4AD fusion


title: Diffuse astrocytoma [DA1]

source_name: Paediartric brain tumour DA1

tag: Sex


title: Sulfur_vs_RCV_III_csw

source_name: Sulfur

value: 50 mM Sulfur


title: Grafted sphere-induced tumour, p53/Pten/Rb background, 3xCATR3

description:
3xCATR3
Dissected brain-derived tumour tissue.

value: p53/Pten/Rb Flox-Hom

value: PNET


title: AdCre-induced tumour, p53/Pten background, 5PCA2

description:
5PCA2
Dissected brain-derived tumour tissue.

value: p53/Pten Flox-Hom

value: oligo-astrocytoma


title: Strain with CTA4-GAL4AD fusion, wild type background, artificially activated CTA4 - log phase - rep2

description:
CTA4-2
Log phase gene expression with the putative hyperactive zinc cluster transcription factor CTA4.


title: Sulfur_vs_RCV_II


title: Strain with CTA4-GAL4AD fusion, wild type background, artificially activated CTA4 - log phase - rep1

description:
CTA4-1
Log phase gene expression with the putative hyperactive zinc cluster transcription factor CTA4.


title: Pilocytic astrocytoma [PA15]

source_name: Paediartric brain tumour PA15

value: Pilocytic astrocytoma

value: I

tag: age


title: Wild type strain - log phase - rep2

description:
SC5314-2
Wild type gene expression in log phase.

source_name: Wild type


title: Pilocytic astrocytoma [PA13]

source_name: Paediartric brain tumour PA13

tag: tissue

value: M


title: Pilocytic astrocytoma [PA14]

source_name: Paediartric brain tumour PA14

value: F


title: AdCre-induced tumour, p53/Pten/Rb background, 3xCA3

description:
3xCA3
Dissected brain-derived tumour tissue.

value: mixed (intercrossed C57, FVB, and mainly 129 Ola)


title: Grafted sphere-induced tumour, p53/Pten/Rb background, 3xCATR2

description:
3xCATR2
Dissected brain-derived tumour tissue.

value: in vitro AdCre-transduced, grafted spheres


title: Grafted sphere-induced tumour, p53/Pten/Rb background, 3xCATR1

description:
3xCATR1
Dissected brain-derived tumour tissue.


title: Pilocytic astrocytoma [PA12]

source_name: Paediartric brain tumour PA12


title: Sulfur_vs_RCV_I


title: Pilocytic astrocytoma [PA11]

source_name: Paediartric brain tumour PA11


title: Wild type strain - log phase - rep3

description:
SC5314-3
Wild type gene expression in log phase.


title: AdCre-induced tumour, p53/Pten/Rb background, 3xCA2

description:
3xCA2
Dissected brain-derived tumour tissue.


title: Sulfite_vs_RCV_III_csw

source_name: Sulfite

value: 5 mM Sulfite


title: Wild type strain - log phase - rep1

description:
SC5314-1
Wild type gene expression in log phase.


title: AdCre-induced tumour, p53/Pten/Rb background, 3xCA1

description:
3xCA1
Dissected brain-derived tumour tissue.


title: Pilocytic astrocytoma [PA10]

source_name: Paediartric brain tumour PA10


title: Sulfide_vs_RCV_II

source_name: Sulfide

value: 4 mM Sulfide


title: Sulfide_vs_RCV_III_csw


title: MCF-7-siRBM38-3

city: Philadelphia

first: Russ

middle: P.

last: Carstens

state: PA

address: 575 Clinical Research Building, 415 Curie Boulevard

department: Renal Division, Department of Medicine

institute: University of Pennsylvania

description: MCF-7 cells treated with siRNA for RBM38, biological rep 3

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Human Exon Junction Arrays according to manufacturer’s protocols at the Penn Microarray Core Facility.

scan_protocol: Hybridized Affymetrix Human Exon Junction Arrays were scanned following the manufacturer’s protocols at the Penn Microarray Core Facility

data_processing: Raw image files were processed using Affymetrix GCOS 1.3 software to generate CEL data files. HJAY array expression indexes were calculated using the ProbeEffects program (Kapur et al., 2007, Genome Biol 8:R82). Briefly, the program employs a sequence-specific background model to correct background intensities of exon-array probes (Kapur et al., 2007, Genome Biol 8:R82), followed by an iterative probe selection procedure (Xing et al., 2006, PLoS ONE 1:e88) that selects a subset of highly correlated probes of a gene for expression index computation. Differential splicing events were detected using the MADS+ algorithm (Shen et al., 2009).

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix Human Exon Junction arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).  Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).

growth_protocol: MCF-7 cells were grown in DMEM-F12 media supplemented with 10% FBS (Thermo Scientific) and Glutamax (Invitrogen).

extract_protocol: Total RNA was collected from adherent tissue culture cells using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).

treatment_protocol: siRNA knockdown of RBM38 in human MCF-7 breast cancer cells cell was performed as described before (Warzecha et al., 2009, Molecular Cell 33:591 - 601).

tag: cell line

value: MCF-7 breast cancer cells

value: RBM38 knockdown


title: MCF-7-siRBM38-4

description: MCF-7 cells treated with siRNA for RBM38, biological rep 4


title: LX2_6.2_rep2

city: Shanghai

first: Wenxin

last: Qin

address: No. 25/Ln 2200 Xie-Tu Road

institute: Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine

description:
Gene expression under different pH
LX-2, pH6.2, 6 days, rep2

hyb_protocol: 1.75 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 110 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 110 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent G3 Human8*60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing:
Gene expression data were extracted using Feature Extraction software and were quantile-normalized using GeneSpring software (Agilent Technologies).
Genes with a fold change ≥1.5 and p-value < 0.05 were considered to be differentially expressed.

source_name: LX-2, pH6.2, 6 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 4 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent), followed by purification with QIAGEN RNeasy® Mini Kit.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer at OD A250, A550 and A650.

growth_protocol: The human hepatic stellate cell line LX-2 was cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco, CA, USA), with 10% Fetal Bovine Serum (Gibco, CA, USA), in a 5% CO2 atmosphere at 37℃.

extract_protocol: Total RNA of LX-2 cells was isolated from cells at 80% confluence with mirVana™ miRNA Isolation Kit (Ambion, Life Technology, MA, USA) and purified using an RNeasy Mini Kit (Qiagen).

treatment_protocol: LX-2 cells cultured in pH 7.2 or pH 6.2 medium separately for six days.

value: healthy hepatic stellate cell line LX-2

tag: ph


title: Sulfite_vs_RCV_II

value: RCV control


title: Thiosulfate_vs_RCV_IV

value: 10 mM Thiosulfate


title: LX2_6.2_rep1

description:
Gene expression under different pH
LX-2, pH6.2, 6 days, rep1


title: Pilocytic astrocytoma [PA9]

source_name: Paediartric brain tumour PA9


title: Sulfur_vs_RCV_IV

value: 50 mM Sulfur


title: LX2_7.2_rep1

description:
Gene expression under different pH
LX-2, pH7.2, 6 days, rep1

source_name: LX-2, pH7.2, 6 days


title: MCF-7-siRBM38-2

description: MCF-7 cells treated with siRNA for RBM38, biological rep 2


title: MCF-7-siControl-4

description: MCF-7 cells treated with siControl, biological rep 4

source_name: MCF-7 cells treated with siControl

value: control


title: Pilocytic astrocytoma [PA7]

source_name: Paediartric brain tumour PA7


title: Pilocytic astrocytoma [PA5]

source_name: Paediartric brain tumour PA5


title: LX2_7.2_rep2

description:
Gene expression under different pH
LX-2, pH7.2, 6 days, rep2


title: Pilocytic astrocytoma [PA6]

source_name: Paediartric brain tumour PA6


title: Array 1_3: 4106a_3 cy5 + FRC_3 cy3

city: Harpenden

first: Chris

last: Bass

state: Hertfordshire

address: West Common

department: Biological Chemistry

institute: Rothamsted Research

hyb_protocol: Two micrograms of each RNA sample was used to generate labeled cRNA, this was prepared, hybridized onto arrays and these were washed and scanned exactly as described in the Agilent Quick Amp Labeling Protocol (Version 5.7) which can be downloaded from http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp11617.aspx.

scan_protocol: Scanned on an Agilent  G2505C scanner Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Myzus persicae

source_name: ten whole aphids 15 days old

growth_protocol: Both M. persicae clones used in this study were originally established from a single parthenogenetic female collected from a field populations and reared on Chinese cabbage leaves (Brassica napus L var chinensis cv Tip-Top) in small plastic box-cages maintained at 18°C under a 16:8 h light:dark regime. Aphids of similar age were regularly transferred to new boxes in order to rear them as distinct cohorts.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Genomic DNA was removed by DNase I digestion using the DNA-free DNase Treatment and Removal Reagent (Ambion).

treatment_protocol: Clones reared as above (both clones were untreated)

tag: clone

value: whole organism

value: FRC


title: MCF-7-siControl-3

description: MCF-7 cells treated with siControl, biological rep 3


title: Array 1_2: 4106a_2 cy5 + FRC_2 cy3

label_protocol: Two micrograms of each RNA sample was used to generate labeled cRNA, this was prepared, hybridized onto arrays and these were washed and scanned exactly as described in the Agilent Quick Amp Labeling Protocol (Version 5.7) which can be downloaded from http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp11617.aspx.


title: Array 1_1: 4106a_1 cy5 + FRC_1 cy3


title: MCF-7-siRBM38-1

description: MCF-7 cells treated with siRNA for RBM38, biological rep 1


title: MCF-7-siControl-2

description: MCF-7 cells treated with siControl, biological rep 2


title: Array 1_3: 4106a_3 cy3 + FRC_3 cy5


title: Sulfide_vs_RCV_IV

source_name: RCV control


title: Sulfite_vs_RCV_IV


title: Pilocytic astrocytoma [PA3]

source_name: Paediartric brain tumour PA3

value: Pilocytic astrocytoma

tag: grade


title: Array 1_4: 4106a_4 cy3 + FRC_4 cy5


title: MCF-7-siControl-1

description: MCF-7 cells treated with siControl, biological rep 1


title: Ependymoma [E4]

source_name: Paediartric brain tumour E4

value: Ependymoma

value: III


title: Array 1_4: 4106a_4 cy5 + FRC_4 cy3


title: Array 1_2: 4106a_2 cy3 + FRC_2 cy5


title: Pilocytic astrocytoma [PA2]

source_name: Paediartric brain tumour PA2

value: I

value: M


title: Array 1_1: 4106a_1 cy3 + FRC_1 cy5


title: Pilocytic astrocytoma [PA1]

source_name: Paediartric brain tumour PA1

value: F


title: White vs Pooled reference, replicate 1

status: Public on Jul 28 2013

city: San Francisco

first: Changbin

last: Chen

state: California

address: HSE450, 513 Parnassus Avenue

department: Department of Microbiology & Immunology

institute: University of California, San Francisco

description: Biological replicate 1 of 2. White vs Pooled reference

hyb_protocol: Equal amount of cDNA from each sample was pooled to prepare the reference mix. Cy5 labeled cDNAs from each strain were directly hybridized against the pooled reference (Cy3).

scan_protocol: Arrays were scanned using a Genepix 4000A Axon scanner, and spots were filtered using GenePix Pro software.

data_processing: Data were normalized using Goulphar (LOWESS normalization) and subjected to Bayesian Analysis of Gene Expression Levels (BAGEL).

source_name: White grown SC

label_protocol: 10 μg of each RNA was treated with DNase I (Turbo DNA-free kit, Ambion) and reverse transcribed using aminoallyl-dUTP and Superscript II (Invitrogen) according to manufacturers’ instructions.  cDNA was labeled with Cy3 and Cy5 (Amersham)

growth_protocol: Saturated overnight cultures of wild type (SN425), white (SN966, a/a), opaque (SN967, a/a), WOR1OE-white and WOR1OE-gut (post-mouse isolates derived from SN928), were inoculated into SC medium (supplemented with 100 g/ml of uridine) to OD600=0.1 and incubated with shaking at room temperature for 6-8 hours before harvesting at OD600=0.8-1.0. 4 biological replicates were performed per strain. Total RNA isolation, cDNA labeling, and array hybridizations were performed as described previously.

extract_protocol: Total RNA was prepared using a hot phenol method (Miller and Johnson, 2002).

tag: strain

source_name: Pooled reference

value: Pooled reference


title: WOR1OE-White vs Pooled reference, replicate 3

description: Biological replicate 3 of 4. WOR1OE-White vs Pooled reference

source_name: WOR1OE-White grown in SC


title: White vs Pooled reference, replicate 2

description: Biological replicate 2 of 2. White vs Pooled reference


title: WOR1OE-GUT vs Pooled reference, replicate 1

description: Biological replicate 1 of 4. WOR1OE-GUT vs Pooled reference

source_name: WOR1OE-GUT grown in SC


title: WOR1OE-White vs Pooled reference, replicate 4

description: Biological replicate 4 of 4. WOR1OE-White vs Pooled reference


title: WOR1OE-GUT vs Pooled reference, replicate 3

description: Biological replicate 3 of 4. WOR1OE-GUT vs Pooled reference


title: WOR1OE-GUT vs Pooled reference, replicate 2

description: Biological replicate 2 of 4. WOR1OE-GUT vs Pooled reference


title: Wild type vs Pooled reference, replicate 4

description: Biological replicate 4 of 4. Wild type vs Pooled reference

source_name: Wild type grown in SC


title: Opaque vs Pooled reference, replicate 2

description: Biological replicate 2 of 2. Opaque vs Pooled reference

source_name: Opaque grown in SC


title: WOR1OE-GUT vs Pooled reference, replicate 4

description: Biological replicate 4 of 4. WOR1OE-GUT vs Pooled reference


title: WOR1OE-White vs Pooled reference, replicate 1

description: Biological replicate 1 of 4. WOR1OE-White vs Pooled reference


title: Opaque vs Pooled reference, replicate 1

description: Biological replicate 1 of 2. Opaque vs Pooled reference


title: WOR1OE-White vs Pooled reference, replicate 2

description: Biological replicate 2 of 4. WOR1OE-White vs Pooled reference


title: Wild type vs Pooled reference, replicate 2

description: Biological replicate 2 of 4. Wild type vs Pooled reference


title: Wild type vs Pooled reference, replicate 1

description: Biological replicate 1 of 4. Wild type vs Pooled reference


title: Wild type vs Pooled reference, replicate 3

description: Biological replicate 3 of 4. Wild type vs Pooled reference


title: reference vs #42

city: Goyang-si

first: Hye-Jin

last: Shin

state: Gyeonggi-do

address: 323 Ilsan-ro, Ilsandong-gu

department: Research Institute and Hospital

country: South Korea

institute: National Cancer Center

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

source_name: Stratagene Human reference RNA

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

extract_protocol: Stratagene Human reference RNA

tag: reference composition

value: pooling RNA from 10 Human cell lines

source_name: Cervical cancer sample #42

extract_protocol: 1. We prepared RNA samples from cervical cancer patients’ frozen tissues. 2. Total RNA was extracted using a TRIzol® (Invitrogen, Carlsbad, CA, USA) method, followed by the clean-up with the RNeasy® Mini kit isolation method (Qiagen GmbH, Hilden, Germany). The purity and integrity of the total RNA were checked using the NanoDrop (NanoDrop Technologies) and the Experion (Biorad), respectively.

value: cervix

tag: disease

value: Cancer

tag: grouping according to hpv dna physical status

value: Group 3_Multicopy tandem repeated integration


title: reference vs #40

source_name: Cervical cancer sample #40

value: Group 1_ Single copy HPV integration with episomal components


title: reference vs #44

source_name: Cervical cancer sample #44


title: PC-3M/MYB siRNA #3

city: Houston

first: Timothy

middle: C.

last: Thompson

state: Texas

address: 1515 Holcombe Blvd.

department: Genitourinary Medical Oncology

institute: MD Anderson Cancer Center

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

source_name: PC-3M/MYB siRNA

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Invitrogen).

extract_protocol: RNA was extracted and prepared with MirVana miRNA Isolation Kit (Invitrogen) in accordance with the prescribed protocol provided with the kit.

value: prostate cancer cell line PC-3M

tag: genotype/variation

value: MYB siRNA


title: reference vs #47

source_name: Cervical cancer sample #47

value: Group 4_ Low HPV


title: reference vs #45

source_name: Cervical cancer sample #45


title: DU145/MYB siRNA #3

source_name: DU145/MYB siRNA

value: prostate cancer cell line DU145


title: reference vs #38

source_name: Cervical cancer sample #38


title: PC-3M/NC siRNA #3

source_name: PC-3M/NC siRNA

value: negative control siRNA


title: reference vs #37

source_name: Cervical cancer sample #37


title: VCaP/MYB siRNA #3

source_name: VCaP/MYB siRNA

value: prostate cancer cell line VCaP


title: VCaP/NC siRNA #3

source_name: VCaP/NC siRNA


title: DU145/NC siRNA #3

source_name: DU145/NC siRNA


title: PC-3M/MYB siRNA #2


title: reference vs #35

source_name: Cervical cancer sample #35


title: LNCaP/MYB siRNA #3

source_name: LNCaP/MYB siRNA

value: prostate cancer cell line LNCaP


title: reference vs #32

source_name: Cervical cancer sample #32


title: reference vs #36

source_name: Stratagene Human reference RNA

source_name: Cervical cancer sample #36


title: reference vs #31

source_name: Cervical cancer sample #31

value: Group 2_ Single copy HPV integration without episomal components


title: DU145/MYB siRNA #2


title: reference vs #30

source_name: Cervical cancer sample #30


title: reference vs #29

source_name: Cervical cancer sample #29


title: PC-3M/NC siRNA #2


title: reference vs #33

source_name: Cervical cancer sample #33


title: LNCaP/NC siRNA #3

source_name: LNCaP/NC siRNA


title: reference vs #34

source_name: Cervical cancer sample #34


title: DU145/NC siRNA #2


title: reference vs #28

source_name: Cervical cancer sample #28


title: VCaP/MYB siRNA #2


title: PC-3M/MYB siRNA #1

source_name: PC-3M/MYB siRNA


title: reference vs #25

source_name: Cervical cancer sample #25


title: reference vs #27

source_name: Cervical cancer sample #27


title: reference vs #24

source_name: Cervical cancer sample #24


title: reference vs #21

source_name: Cervical cancer sample #21


title: PC-3M/NC siRNA #1

source_name: PC-3M/NC siRNA


title: reference vs #22

source_name: Cervical cancer sample #22


title: reference vs #26

source_name: Cervical cancer sample #26


title: reference vs #39

source_name: Stratagene Human reference RNA

source_name: Cervical cancer sample #39


title: VCaP/NC siRNA #2

source_name: VCaP/NC siRNA


title: LNCaP/MYB siRNA #2

source_name: LNCaP/MYB siRNA


title: LNCaP/NC siRNA #2


title: reference vs #20

source_name: Cervical cancer sample #20


title: DU145/NC siRNA #1

source_name: DU145/NC siRNA


title: Pilocytic astrocytoma [PA8]

city: London

source_name: Paediartric brain tumour PA8

extract_protocol: RNA was extracted with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: Pilocytic astrocytoma

value: I


title: reference vs #18

source_name: Cervical cancer sample #18


title: reference vs #16

source_name: Cervical cancer sample #16


title: DU145/MYB siRNA #1

source_name: DU145/MYB siRNA


title: VCaP/MYB siRNA #1

source_name: VCaP/MYB siRNA


title: LNCaP/MYB siRNA #1


title: CWR/CSS/NC siRNA #3

source_name: CWR/CSS/NC siRNA

tag: growth protocol

value: CSS

value: prostate cancer cell line CWR22Rv1


title: reference vs #17

value: pooling RNA from 10 Human cell lines

source_name: Cervical cancer sample #17


title: reference vs #12

source_name: Cervical cancer sample #12

value: cervix


title: CWR/RM/AR siRNA #3

source_name: CWR/RM/AR siRNA

value: RM

value: AR siRNA


title: reference vs #15

source_name: Cervical cancer sample #15

value: Cancer

value: Group 1_ Single copy HPV integration with episomal components


title: reference vs #14

source_name: Cervical cancer sample #14


title: CWR/CSS/AR siRNA #3

source_name: CWR/CSS/AR siRNA


title: LNCaP/NC siRNA #1

source_name: LNCaP/NC siRNA


title: CWR/RM/NC siRNA #3

source_name: CWR/RM/NC siRNA


title: reference vs #11

source_name: Stratagene Human reference RNA

source_name: Cervical cancer sample #11


title: VCaP/CSS/AR siRNA #3

source_name: VCaP/CSS/AR siRNA


title: VCaP/NC siRNA #1

source_name: VCaP/NC siRNA


title: VCaP/CSS/NC siRNA #3

source_name: VCaP/CSS/NC siRNA


title: reference vs #10

source_name: Cervical cancer sample #10


title: VCaP/RM/NC siRNA #3

source_name: VCaP/RM/NC siRNA


title: LNCaP/CSS/AR siRNA #3

source_name: LNCaP/CSS/AR siRNA


title: MiaPaCa2 pCEP4 clone 5

first: Hannah

last: Whiteman

address: Charterhouse Square

institute: QMUL

description: gene expression data from pancreatic cancer cell line MiaPaCa2 stabley transfected with empty vector pCEP4

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: RMA robust multi-array analysis using R

source_name: pancreatic cancer cell line MiaPaCa2 containing empty vector pCEP4

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

growth_protocol: MiaPaCa2 stable cell lines were maintained in DMEM with 10% FBS

extract_protocol: extraction of total RNA was performed using Ambion RNAqueous kit according to the manufacturer's instructions

treatment_protocol: cells were grown to 70-80% confluence before RNA extraction.


title: CWR/CSS/AR siRNA #2


title: VCaP/RM/AR siRNA #3

source_name: VCaP/RM/AR siRNA


title: reference vs #6

source_name: Cervical cancer sample #6


title: LNCaP/RM/NC siRNA #3

source_name: LNCaP/RM/NC siRNA


title: LNCaP/CSS/NC siRNA #3

source_name: LNCaP/CSS/NC siRNA


title: LNCaP/RM/AR siRNA #3

source_name: LNCaP/RM/AR siRNA


title: MiaPaCa2 pCEP4 - AGR2 clone 16

description: gene expression data from pancreatic cancer cell line MiaPaCa2 stabley transfected with AGR2 overexpressing vector pCEP4 -AGR2

source_name: pancreatic cancer cell line MiaPaCa2 containing AGR2 overexpressing vector pCEP4 -AGR2


title: reference vs #8

source_name: Cervical cancer sample #8


title: reference vs #4

source_name: Cervical cancer sample #4

value: Group 3_Multicopy tandem repeated integration


title: reference vs #5

source_name: Stratagene Human reference RNA

source_name: Cervical cancer sample #5


title: MiaPaCa2 pCEP4 clone 3

tag: pancreatic cancer cell line MiaPaCa2 stabley transfected with empty vector pCEP4


title: CWR/RM/NC siRNA #2

source_name: CWR/RM/NC siRNA


title: reference vs #9

source_name: Cervical cancer sample #9


title: MiaPaCa2 pCEP4 - AGR2 clone 2

tag: pancreatic cancer cell line MiaPaCa2 stabley transfected with AGR2 overexpressing vector pCEP4 -AGR2


title: FA6 transiently transfected with non-targeting siRNA, transfection B

description: gene expression data frompancreatic cancer cell line FA6 transiently transfected with non-targeting siRNA

growth_protocol: FA6 cells were maintained in DMEM with 10% FBS

treatment_protocol: cells were transfected with siRNA using INTERFERin 48 hours before RNA extraction.


title: MiaPaCa2 pCEP4 - AGR2 clone 15


title: CWR/CSS/NC siRNA #2

source_name: CWR/CSS/NC siRNA


title: MiaPaCa2 pCEP4 clone 1


title: CWR/RM/AR siRNA #2

source_name: CWR/RM/AR siRNA


title: FA6 transiently transfected with non-targeting siRNA, transfection C

source_name: pancreatic cancer cell line FA6 transiently transfected with non-targeting siRNA


title: FA6 transiently transfected with non-targeting siRNA, transfection A

tag: pancreatic cancer cell line FA6 transiently transfected with non-targeting siRNA


title: VCaP/CSS/NC siRNA #2

source_name: VCaP/CSS/NC siRNA


title: reference vs #3

source_name: Cervical cancer sample #3


title: ChIP-Seq H3 USP49 knockdown

type: SRA

city: Richmond

first: Hengbin

last: Wang

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University

library_source: genomic

data_processing:
Basecalls for both RNA-Seq and ChIP-Seq were performed in Illumina 1.5 software.
RNA-Seq and ChIP-seq files were were mapped to hg18 using TopHat (RNA-seq) or Bowtie (ChIP-seq).  Samtools and Picard were used for post alignment processing.
FPKM and transcript sizes were determined using Cufflinks with default settings.
Genome_build: hg18
Supplementary_files_format_and_content: Mapped reads were converted to bedgraph format (BEDTools) and normalized as reads per million total unique mapped reads using the -scale parameter. GTF files for control assembled transcripts and Usp49 knockdown assembled transcripts.

source_name: colorectal carcinoma

growth_protocol: HCT116 USP49 tetracycline inducible knockdown cells (T-Rex Expression System) were grown in DMEM supplemented with 10% FBS, 1% Pennicillin and Streptomycine, blasticidin and puromycin.

extract_protocol: For RNA-Seq, mRNA was specifically enriched from total RNA using oligo(dT) beads and sheared into small pieces.  The fragments were then reverse-transcribed into first-strand cDNA using random hexamer primers, followed by second strand synthesis using DNA polymerase I.  The short cDNA strands were ligated with 3' and 5' adapters for amplification and sequencing.  For ChIP-seq, uninduced control and induced knockdown cells were crosslinked with 1% formaldehyde and chromatin was disrupted into 100-400 bp fragments by sonication and precipitated with either anti-uH2B or anti-H2B antibodies.  After elution from the beads and reverse cross-linking, the DNA fragments were extracted with phenol/chloroform and recovered by ethanol precipitation.  Immunoprecipitated DNA was ligated with 3' and 5' adapters for amplification and sequencing.

treatment_protocol: USP49 knockdown was induced by adding doxycycline to growth media.  Cells were harvested 36 hours after doxycycline induction.

tag: chip antibody

value: anti-H3 (Abcam #1791)


title: VCaP/RM/AR siRNA #2

source_name: VCaP/RM/AR siRNA


title: FA6 transiently transfected with AGR2 siRNA, transfection A

description: gene expression data frompancreatic cancer cell line FA6 transiently transfected with AGR2 siRNA


title: VCaP/RM/NC siRNA #2

source_name: VCaP/RM/NC siRNA


title: LNCaP/CSS/NC siRNA #2

source_name: LNCaP/CSS/NC siRNA


title: LNCaP/CSS/AR siRNA #2

source_name: LNCaP/CSS/AR siRNA


title: FA6 transiently transfected with AGR2 siRNA, transfection B

source_name: pancreatic cancer cell line FA6 transiently transfected with AGR2 siRNA


title: CWR/CSS/NC siRNA #1


title: CWR/RM/NC siRNA #1


title: VCaP/CSS/AR siRNA #2

source_name: VCaP/CSS/AR siRNA


title: VCaP/CSS/AR siRNA #1


title: VCaP/CSS/NC siRNA #1


title: LNCaP/RM/AR siRNA #2

source_name: LNCaP/RM/AR siRNA


title: LNCaP/RM/NC siRNA #2

source_name: LNCaP/RM/NC siRNA


title: LNCaP/RM/AR siRNA #1


title: VCaP/RM/AR siRNA #1


title: LNCaP/RM/NC siRNA #1


title: CWR/RM/AR siRNA #1


title: VCaP/RM/NC siRNA #1


title: LNCaP/CSS/NC siRNA #1


title: CWR/CSS/AR siRNA #1

source_name: CWR/CSS/AR siRNA


title: FA6 transiently transfected with AGR2 siRNA, transfection C

tag: pancreatic cancer cell line FA6 transiently transfected with AGR2 siRNA


title: LNCaP/CSS/AR siRNA #1


title: reference vs #1

source_name: Stratagene Human reference RNA

source_name: Cervical cancer sample #1


title: G8

status: Public on Jul 27 2013

city: Oslo

first: Cecilie

middle: Jonsgar

last: Sandberg

address: Sognsvannsveien 20

department: Neurosurgery

country: Norway

institute: Oslo Univercity Hospital

hyb_protocol: The DIG-labelled cRNA (10 µg) was fragmented and hybridized to Applied Biosystems Human Genome Survey Microarray V2.0 (Applied Biosystems) according to the manufacturer`s protocol (Applied Biosystems Chemiluminesence Detection Kit).

scan_protocol: The slides were scanned using ABI 1700 Chemiluminescent Microarray Analyzer.

data_processing: Initial analysis was done in J-Express 2.8b (Molmine). After removal of flags and control spots the arrays were quantile normalized and log2-transformed.

label: DIG

source_name: glioma stem cells

label_protocol: RNA of each sample was reversely transcribed and amplified and DIG- labelled using the NanoAmp RT-IVT Labelling Kit (Applied Biosystems).

growth_protocol: Biopsy specimens were obtained from informed and consenting patients, and the tissue harvesting was approved by the Norwegian National Committee for Medical Research Ethics (07321b). Biopsies were put in ice cold Leibowitz-15 medium (L15, Invitrogen, Carlsbad, CA). Typically, a biopsy was washed in L-15 and mechanically dissociated using two scalpels. Dissociation into single cells was achieved by either incubation in Trypsin-EDTA (Invitrogen) (tumour tissue) or papain (Worthington Biochemical Corporation) (brain tissue). Thereafter, the enzyme activity was blocked using 2 mg/ml human albumin (Octapharma Pharmazeutika Produktionges, Wien, Austria) and washed in L-15 twice, before the cells were transferred to proliferation medium containing basic fibroblast growth factor (bFGF) 10 ng/ml, epidermal growth factor (EGF) 20 ng/ml (both R&D Systems, Minneapolis, MN), Leukemia inhibitory factor 10ng/ml (Millipore, Billerica, MA), B27-supplement 1:50 (Invitrogen), Penicillin/Streptomycin 100 U/ml of both (Lonza, Basel, Switzerland), Heparin 1 ng/ml (Leo Pharma, Ballerup, Denmark), and Hepes 8 mM (Lonza) in Dulbecco’s modified essential medium with nutrient mix F-12 and Glutamax (DMEM/F12) (Invitrogen). Cells where then incubated at 105 cells/ml in a 75 cm2 non-treated cell culturing flask (Nunc, Roskilde, Denmark). Cells in culture proliferated as free-floating spheres. When spheres reached a size where the core of the spheres turned dark (70-100 µm) cultures were enzymatically digested to single cells. Cells where then replated at 5 x 104 cells/ml.  The secondary spheres from each primary culture were harvested for RNA isolation.

extract_protocol: Total RNA from spheres was isolated using Qiazol and the RNeasy Micro Kit (Qiagen GmbH, Hilden, Germany).  The concentration of each RNA sample was determined by using the Nanodrop spectrophotometer and analyzed for quality using an Agilent 2100 Bioanalyzer with the RNA Nano Assay. Only RNA samples with a RIN value >8 were included for further analysis.

tag: cell type

value: glioma stem cells

tag: origin

value: primary glioblastoma tissue

tag: tumour stage

value: primary glioblastoma

tag: age

tag: Sex

value: F


title: G3


title: G6

value: M


title: G4


title: Pinneaple replica 4

city: Moncada

first: Gema

last: Ancillo

state: Valencia

address: Ctr. Moncada-Naquera Km 4.5

department: Protección Vegetal y Biotecnología

country: Spain

institute: Instituto Valenciano de Investigaciones Agrarias (IVIA)

description: Meristems of juvenile Pineapple sweet orange (C. sinensis (L.) , labeled with Cy3,  compared to meristems of adult Pineapple sweet orange (C. sinensis (L.) , labeled with Cy5; replica 4

hyb_protocol: Microarray hybridisation and washing were performed as described by Martinez-Godoy et al. (2008).

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-nm resolution and 100% laser power.

data_processing: The data were global median normalized using GenePix Pro 6.0 (Axon Molecular Devices) and LOWESS correction was applied using the Acuity 4.0 software (Axon Molecular Devices). Spots with a net intensity in both channels below twofold the mean background intensity were considered low-signal spots and removed. To detect differentially expressed genes, data were analyzed with the Significance Analysis of Microarray package (Tusher et al. 2001) using two-class unpaired comparison.

organism: Citrus sinensis

label_protocol: RNA was labelled following an indirect method (Randolph and Waggoner, 1997). Reverse transcription, cDNA purification, dye coupling and fluorescent cDNA purification was accomplished as described by Forment et al. (2005), except that total RNA (40 ug) was used instead of poly(A)+ RNA.

growth_protocol: Plants were growth in a temperature-controlled (18°C night and 26ºC day) greenhouse.

extract_protocol: Total RNA was extracted from meristems using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: Wild type plants of two different developmental stages (juvenile and adult) were compared

tag: developmental stage

value: juvenile

source_name: Meristems of adult Pineapple sweet orange (C. sinensis (L.)

value: adult


title: G9


title: G5


title: H3

source_name: adult neural stem cells

value: adult neural stem cells

value: subventricular zone, human brain tissue

value: Normal


title: Pinneaple replica 2

description: Meristems of juvenile Pineapple sweet orange (C. sinensis (L.) , labeled with Cy3,  compared to meristems of adult Pineapple sweet orange (C. sinensis (L.) , labeled with Cy5; replica 2


title: G7


title: WT CD4SP thymocytes 1

city: Bethesda

first: Jung-Hyun

last: Park

state: MD

address: 10 Center Dr

department: EIB

institute: NIH/NCI

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control ratios.

label: SYBR Green

source_name: WT CD4SP thymocytes

label_protocol: PCR assays were performed using sorted CD4SP thymocytes and the apoptosis or program cell death PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. RNA was reverse transcribed into cDNA by oligo(dT) priming with the QuantiTect Reverse transcription kit (Qiagen). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: total TCRbhiCD4+CD8-

tag: activation agent

value: fresh

value: wild type


title: 4 dpp Polysome  translating, biological rep3

city: Greenville

first: Christopher

middle: B

last: Geyer

state: NC

address: 600 Moye Boulevard, Mail Stop 620

department: Anatomy and Cell Biology

institute: East Carolina University

description: Gene expression data from 4 dpp mouse testes translating mRNAs

hyb_protocol: Hybridized to the Affymetrix 430 2.0 mouse expression array at the core facility at the University of North Carolina, Neuroscience Research Center, Chapel Hill, NC.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G Plus Targeted Genotyping System.

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

source_name: Mouse 4 dpp testes translating mRNAs

label_protocol: Biotin-labeled amplified antisense RNA was synthesized from 5 ug of RNA by the standard Affymetrix 3’ IVT procedure

growth_protocol: All animal procedures were performed in accordance with the National Research Council Guide for the Care and Use of Laboratory Animals and approved by the Animal Care and Use Committee of East Carolina University. CD-1 mice were used for all analyses. Euthanasia was performed by decapitation, and testes were snap-frozen in liquid nitrogen and stored at -80°C.

extract_protocol: RNA was isolated from polysome sucrose fractions by TRIzol extraction (Invitrogen) using manufacturer’s instructions

treatment_protocol: Testes were harvested and washed with 1X ice-cold phosphate-buffered saline (PBS) containing cycloheximide to freeze polysomes, then immediately snap-frozen in liquid nitrogen, and stored at -80°C. Testes were pulverized under liquid nitrogen and lysed in 1 ml polysome lysis. Lysates were homogenized and nuclei were pelleted by centrifugation. Cytoplasmic extracts were layered onto a linear sucrose density gradient in polysome gradient and then centrifuged at 210,000 x g at 4°C for 2 h without braking. Gradients were then fractionated using an ISCO gradient fractionation system equipped with a UA-6 detector. RNP fractions, 40S, 60S, 80S, light polysomes, and heavy polysomes were monitored by continuous UV absorption profiles at 254 nm. Fourteen successive 750 μl fractions were collected and stored at -80°C.

tag: tissue

value: Testis

tag: genotype

value: 4 days post partium


title: H5


title: H1


title: H4


title: G2


title: G1


title: H2


title: 4 dpp Polysome  translating, biological rep2


title: 4 dpp Non-translating, biological rep3

description: Gene expression data from 4 dpp mouse testes non-translating mRNAs

source_name: Mouse 4 dpp testes non-translating mRNAs


title: 4 dpp Polysome  translating, biological rep1


title: WT CD4SP thymocytes 2

description: Control


title: Ik7Tg CD4SP thymocytes 4

description: Test

source_name: Ik7Tg CD4SP thymocytes


title: Ik7Tg CD4SP thymocytes 3

description: Test


title: 4 dpp Non-translating, biological rep2


title: 4 dpp Non-translating, biological rep1


title: 1 dpp Polysome  translating, biological rep3

description: Gene expression data from 1 dpp mouse testes translating mRNAs

source_name: Mouse 1 dpp testes translating mRNAs

value: 1 day post partium


title: 1 dpp Polysome  translating, biological rep2


title: Pinneaple replica 3

description: Meristems of juvenile Pineapple sweet orange (C. sinensis (L.) , labeled with Cy5,  compared to meristems of adult Pineapple sweet orange (C. sinensis (L.) , labeled with Cy3; replica 3


title: Pinneaple replica 1

description: Meristems of juvenile Pineapple sweet orange (C. sinensis (L.) , labeled with Cy5,  compared to meristems of adult Pineapple sweet orange (C. sinensis (L.) , labeled with Cy3; replica 1


title: WT mature CD4SP thymocytes 2

description: Control

value: mature TCRbhiHSAloCD4+CD8-


title: Rough lemon replica 2

description: Meristems of juvenile rough lemon (C. jambirhi Lush.) , labeled with Cy3,  compared to meristems of adult rough lemon (C. jambirhi Lush.) , labeled with Cy5; replica 2

organism: Citrus jambhiri

source_name: Meristems of adult rough lemon (C. jambirhi Lush.)


title: Ik7Tg mature CD4SP thymocytes 3

description: Test


title: Ik7Tg mature CD4SP thymocytes 4

description: Test


title: Rough lemon replica 1

description: Meristems of juvenile rough lemon (C. jambirhi Lush.) , labeled with Cy5,  compared to meristems of adult rough lemon (C. jambirhi Lush.) , labeled with Cy3; replica 1


title: Ik7Tg immature CD4SP thymocytes 3

description: Test

value: immature TCRbhiHSAhiCD4+CD8-


title: WT immature CD4SP thymocytes 1

description: Control


title: 1 dpp Polysome  translating, biological rep1


title: WT immature CD4SP thymocytes 2

description: Control


title: Ik7Tg immature CD4SP thymocytes 4

description: Test


title: Rough lemon replica 3

description: Meristems of juvenile rough lemon (C. jambirhi Lush.) , labeled with Cy5,  compared to meristems of adult rough lemon (C. jambirhi Lush.) , labeled with Cy3; replica 3


title: WT mature CD4SP thymocytes 1

description: Control


title: Rough lemon replica 4

description: Meristems of juvenile rough lemon (C. jambirhi Lush.) , labeled with Cy3,  compared to meristems of adult rough lemon (C. jambirhi Lush.) , labeled with Cy5; replica 4