title: CYC ChIP ZT14

status: Public on Nov 15 2011

city: Waltham

first: Katharine

last: Abruzzi

state: MA

address: 415 South St.

institute: Brandeis University; Howard Hughes Medical Institute

description: 3 repeats of a CYC CHIP-chip in CYC-3FLAG flies  (test=ChIP sample; ctrl: Input)

hyb_protocol: ChIP samples were hybridized to Drosophila 2.0 Tiling Arrays exactly as described in manufacturers instructions.  See www.affymetrix.com/support/.../chromatin_immun_ChIP.pdf

scan_protocol: Drosophila 2.0 Tiling Arrays were scanned via a Gene CHIP Scanner 3000 (Affymetrix) and the GeneCHIP Operating Software version 1.4.

data_processing: To identify significant peaks of CLK, CYC, PER, and Pol II binding throughout the genome Affymetrix .CEL files for both input and IP samples from two or more independent experiments were analyzed using MAT (Johnson et al. 2006).

organism: Drosophila melanogaster

source_name: CYC ChIP DNA from CYC-3FLAG flies

label_protocol: ChIP samples were labeled exactly as described in manufacturers instructions.  See www.affymetrix.com/support/.../chromatin_immun_ChIP.pdf

growth_protocol: Drosophila were entrained for 3-4 days in 12:12 light:dark conditions.  Flies were harvested at the appropriate time (see above).

extract_protocol: ChIP protocol was based on previous protocol (Yu et al. 2006) with modifications. yw;;Clk-V5, yw; GMR-hid; Clk-V5 or CYC-3FLAG flies were entrained for three days in LD conditions and then collected every four hours. 1ml of fly heads were homogenized in 3ml of NEB buffer (10mM Hepes-Na pH8.0, 10mM NaCl, 0.1mM EGTA-Na pH 8.0, 0.5mM EDTA-Na pH 8.0, 1mM DTT, 0.5% Tergitol NP-10, 0.5mM Spermidine, 0.15mM Spermine plus protease inhibitor tablets (Roche)) for a total of 30 minutes (10 X 2’ homogenization, 1’ on ice). Homogenate was dumped into a 70µM cell strainer placed in a 50ml falcon tube and centrifuged at 300g for 1 minute. Filtered homogenate was centrifuged at 6000g for 10 minutes. The nuclei-containing pellets were resuspended in 1ml of NEB and centrifuged for 20’ at 20,000g on sucrose gradient (0.65ml of 1.6M Sucrose in NEB and 0.35ml of 0.8M Sucrose in NEB). The pellet was resuspended in 1ml NEB and 11% Formaldehyde (diluted in Schneider’s media (Sigma)) was added to a final concentration of 1%. Nuclei were crosslinked at room temperature for 10’ before crosslinking was quenched by adding 1/10 vol. of 1.375M glycine. The nuclei were collected by centrifugation at 6000g for 5’. Nuclei were washed twice in 1ml NEB and resuspended in 450µl of Sonication buffer (10mM HEPES-Na pH7.5, 2mM EDTA pH8.0, 1% SDS, 0.2% Trition X-100, 0.5mM Spermidine, 0.15mM Spermine). Nuclei were sonicated using a Fisherbrand Sonic Dismembranator at setting 2 (57 watts) for 4 x 15’’ on; 2’ on ice. Sonicated nuclei were centrifuged at 15,000 g for 10’ and frozen at -80°C in 150µl aliquots. The majority of the sonicated chromatin was ~500-1000bp length.  25µl of sonicated chromatin was removed for the input sample. The remaining 125µl of chromatin was diluted in 1.1ml of IP buffer (50mM HEPES/KOH pH7.6, 2mM EDTA, 1% Triton, 0.1% NaDeoxycholate in PBS). Samples were rotated overnight at 4°C after adding antibodies: 15µl anti-V5 antibody (Abcam ab9116), 1µl of anti-PER antibody (Dembinska et al. 1997) or 1µl of anti-Pol II antibody (gift from A. Greenleaf). Protein G-Sepharose beads (Zymed) were blocked overnight in 0.1mg/ml yeast tRNA and 1mg/ml BSA in IP buffer. For CYC IPs, 25µl of Anti-FLAG M2 Affinity Gel (Sigma A2220) blocked overnight and then incubated with chromatin for 3 hours.  After overnight incubation, the beads were washed 1x in IP buffer, added to the chromatin/antibody mixture, and then incubated at 4°C for an additional 2 hours. Beads were spun down for 20s at 10,000 rpm and washed 1x in 1.5ml ChIP Wash buffer (50mM HEPES-KOH pH7.6, 1mM EDTA, 1% Triton, 0.1% NaDeoxycholate, 0.1% Sarkosyl, 0.1% BSA, 0.5M KCl in PBS). Beads were resuspended in 1ml ChIP Wash buffer and rotated for 30’ at 4°C. Beads were then washed 1x in Li Wash Buffer (10mM Tris-Cl pH8.0, 0.25M LiCl, 0.5% NP40, 0.5% NaDeooxychoalte, 1mM EDTA) and 1x in cold TE pH8.0 before being eluted with 150µl of ChIP Elution buffer (50mM Tris-HCl pH8.0, 10mM EDTA, 1% SDS, 1mM DTT, 0.1mg/ml Proteinase K). 150µl of ChIP Elution buffer was also added to the input sample. Both IP and Input samples were incubated at 37°C for 2 hours. The sepharose beads were removed from the IP samples and then all samples were decrosslinked at 65°C overnight. DNA was isolated from the samples using PCR purification kit (Qiagen).

treatment_protocol: Flies were frozen on dry ice and heads isolated.

value: whole organism

tag: zt time

tag: chip antibody

value: CYC

tag: chip antibody manufacturer

value: Sigma

tag: chip antibody catalog #

source_name: ZT14 Input DNA from CYC-3FLAG flies


title: low-milk yield vs high-milk yield biological rep 3, tech rep 1

status: Public on Nov 16 2011

type: RNA

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

description: Biological replicate 3 of 4, technical replicate 1 of 2

hyb_protocol: Standard Agilent hybridization protocol.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Background correction method normexp was used and followed by loess method for within array normalization. Between array normalization was performed with the Aquantile method. Mean values of channels intensities were taken as an input and a median of background signal for background correction calculations.

molecule: total RNA

organism: Bos taurus

source_name: quarter of mammary gland

label_protocol: 1000 ng of total RNA was labeled using Quick Amp Labeling Kit, two color with Cy5 i Cyc 3 (Agilent) according to manufacturer’s protocol.

extract_protocol: Total RNA was isolated using (RNeasy Mini Kit Qiagen, Germany), separately from quarter of mammary gland according to the manufacturer’s protocol. Quantity and quality of each RNA sample was estimated by Nanodrop (Nanodrop, USA) and Bioanalyzer (Agilent, USA).

tag: breed

value: Holstein Friesian

tag: individual/probe/cow number

tag: lactation

value: low-milk yield IV

value: high-milk yield IV


title: Pol II ChIP ZT18

type: genomic

department: Biology

country: USA

description: 2 repeats of a POL CHIP-chip at ZT18 (test=ChIP sample; ctrl: Input)

label: Biotin

molecule: genomic DNA

source_name: Pol II ChIP DNA from CLK-V5 flies

tag: genotype

tag: tissue

value: Pol II

value: A. Greenleaf

source_name: ZT18 Input DNA from CLK-V5 flies


title: Pol II ChIP ZT6

description: 2 repeats of a POL CHIP-chip at ZT6 (test=ChIP sample; ctrl: Input)

source_name: ZT6 Input DNA from CLK-V5 flies


title: Pol II ChIP ZT10

description: 2 repeats of a POL CHIP-chip at ZT10 (test=ChIP sample; ctrl: Input)

source_name: ZT10 Input DNA from CLK-V5 flies


title: Pol II ChIP ZT2

description: 2 repeats of a POL CHIP-chip at ZT2 (test=ChIP sample; ctrl: Input)

source_name: ZT2 Input DNA from CLK-V5 flies


title: Pol II ChIP ZT14

description: 2 repeats of a POL CHIP-chip at ZT14 (test=ChIP sample; ctrl: Input)

source_name: ZT14 Input DNA from CLK-V5 flies


title: PER ChIP ZT18

description: 2 repeats of a PER CHIP-chip at ZT18 (test=ChIP sample; ctrl: Input)

source_name: PER ChIP DNA from CLK-V5 flies

value: PER

value: Dembinska et al. 1997


title: CLK ChIP ZT14 WT

description: 2 repeats of a CLK CHIP-chip at ZT14 in WT bkgd performed side-by-side with GMR-hid sample  (test=ChIP sample; ctrl: Input)

source_name: CLK ChIP DNA from CLK-V5 flies for GMR experiments

value: yw;;Clk-V5 GMR-hid

value: Abcam


title: human neural progenitor cell line Control_siRNA replicate2

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

country: United Kingdom

institute: Cardiff University

description: SAMPLE 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Sample probe profile were exported from GenomeStudio. Data were then imported into lumi (bioconductor) and Variance Stabilizing transformation applied, Robust Spline Normalized and log2 transformed.

organism: Homo sapiens

source_name: CTXOE03 cell line; Control_siRNA

label_protocol: Biotinylated cDNA were prepared using the Custom Illumina® TotalPrep™-96 Kit (Ambion)

growth_protocol: Cells were maintained as described by Pollock K et al, Exp Neurol. 2006 May;199(1):143-55.

extract_protocol: Standard Trizol extraction followed by DNase treatment, RNA dissolved in water.

treatment_protocol: Transfection of Stealth siRNA (Invitrogen), either control or two separate siRNAs targeting ZNF804A (HSS150612 or HSS150613) using the N-Ter transfection system(Sigma). Cells were harvested using acutase 4 days after transfection.

tag: cell line

value: CTXOE03 cell line

tag: cell type

value: Neural progenitor

tag: brain region of origin

value: Fetal cortical neuroepithelium

tag: gender

value: Male


title: PER CHIP ZT22

description: 2 repeats of a PER CHIP-chip at ZT22 (test=ChIP sample; ctrl: Input)

source_name: ZT22 Input DNA from CLK-V5 flies


title: CLK ChIP ZT14 GMR-hid

description: 2 repeats of a CLK CHIP-chip at ZT14 in GMR-hid  (test=ChIP sample; ctrl: Input)

source_name: CLK ChIP DNA from GMR-hid, CLK-V5 flies

value: yw; GMR-hid

source_name: ZT14 Input DNA from GMR-hid;CLK-V5 flies


title: human neural progenitor cell line Control_siRNA replicate1

description: SAMPLE 1


title: Pol II ChIP ZT22

description: 2 repeats of a POL CHIP-chip at ZT22 (test=ChIP sample; ctrl: Input)

value: whole organism


title: high-milk yield vs low-milk yield biological rep 3, tech rep 2

description: Biological replicate 3 of 4, technical replicate 2 of 2


title: PER ChIP ZT10

description: 2 repeats of a PER CHIP-chip at ZT10 (test=ChIP sample; ctrl: Input)


title: PER ChIP ZT6

description: 2 repeats of a PER CHIP-chip at ZT6 (test=ChIP sample; ctrl: Input)


title: PER ChIP ZT14

description: 2 repeats of a PER CHIP-chip at ZT14 (test=ChIP sample; ctrl: Input)


title: human neural progenitor cell line Control_siRNA replicate4

description: SAMPLE 4


title: CLK ChIP ZT22

description: 2 repeats of a CLK CHIP-chip at ZT22 (test=ChIP sample; ctrl: Input)

source_name: CLK ChIP DNA from CLK-V5 flies


title: PER CHIP ZT2

description: 2 repeats of a PER CHIP-chip at ZT2 (test=ChIP sample; ctrl: Input)


title: CLK ChIP ZT14

description: 2 repeats of a CLK CHIP-chip at ZT14 (test=ChIP sample; ctrl: Input)


title: CLK ChIP ZT18

description: 2 repeats of a CLK CHIP-chip at ZT18 (test=ChIP sample; ctrl: Input)


title: CLK ChIP ZT10

description: 2 repeats of a CLK CHIP-chip at ZT10 (test=ChIP sample; ctrl: Input)


title: low-milk yield vs high-milk yield biological rep 2, tech rep 1

description: Biological replicate 2 of 4, technical replicate 1 of 2

value: low-milk yield II

value: high-milk yield II


title: CLK ChIP ZT2

description: 2 repeats of a CLK CHIP-chip at ZT2 (test=ChIP sample; ctrl: Input)


title: high-milk yield vs low-milk yield biological rep 1, tech rep 2

description: Biological replicate 1 of 4, technical replicate 2 of 2

value: Holstein Friesian


title: CLK ChIP ZT6

description: 2 repeats of a CLK CHIP-chip at ZT6 (test=ChIP sample; ctrl: Input)


title: low-milk yield vs high-milk yield biological rep 1, tech rep 1

description: Biological replicate 1 of 4, technical replicate 1 of 2


title: 24 hours glucocorticoid treated NALM6 cells, experiment 3

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description:
0908_001_NALM24p3_E01_MB_141207
Gene expression profile 24 hours glucocorticoid treated NALM6 preB-ALL cells, experiment 3

hyb_protocol: Target samples were hybridized to Human Exon 1.0 ST v2 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data was preprocessed using the GCRMA method (option GSB.adjust set to FALSE). For transcript probe set definition a custom CDF package was used, that was based on a complete re-alignment of the Exon microarray oligo-probes and annotation to Ensembl version 58.

label: biotin

source_name: NALM6 precursor B-ALL cell line

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: PreB-ALL NALM6 cells were cultured in RPMI 1640 supplemented with 10% fetal calf serum and 2mM L-glutamine at 37C, 5% carbon-dioxide and saturated humidity.

extract_protocol: Total RNA was extracted usinf the TRIZOL protocol according to the manufacturer's protocol, depleted of ribosomal RNA and transcribed into cDNA using T7-promoter-tagged hexamer primers. Antisense RNA was produced by T7-polymerase and transcribed into cDNA using random priming in the presence of dUTP which was used to enzymatically fragment the cDNA.

treatment_protocol: Cells were treated in 3 independent experiments with 100nM dexamethasone (a synthetic glucocorticoid) or 0.1% ethanol as empty carrier control.

value: NALM6 precursor B-ALL

tag: treatment

value: dexamethasone

tag: time [hours]


title: 24 hours glucocorticoid treated NALM6 cells, experiment 1

description:
0916_001_NALM24p1_E01_MB_191207
Gene expression profile 24 hours glucocorticoid treated NALM6 preB-ALL cells, experiment 1


title: 24 hours glucocorticoid treated NALM6 cells, experiment 2

description:
0906_001_NALM24p2_E01_MB_141207
Gene expression profile 24 hours glucocorticoid treated NALM6 preB-ALL cells, experiment 2


title: 24 hours ethanol treated NALM6 cells, experiment 3

description:
0907_001_NALM24m3_E01_MB_141207
Gene expression profile 24 hours ethanol treated NALM6 preB-ALL cells, experiment 3

value: ethanol


title: 24 hours ethanol treated NALM6 cells, experiment 2

description:
0905_001_NALM24m2_E01_MB_141207
Gene expression profile 24 hours ethanol treated NALM6 preB-ALL cells, experiment 2


title: 24 hours ethanol treated NALM6 cells, experiment 1

description:
0915_001_NALM24m1_E01_MB_191207
Gene expression profile 24 hours ethanol treated NALM6 preB-ALL cells, experiment 1


title: 6 hours glucocorticoid treated NALM6 cells, experiment 2

description:
0899_001_NALM6p2_E01_MB_071207
Gene expression profile 6 hours glucocorticoid treated NALM6 preB-ALL cells, experiment 2


title: 6 hours ethanol treated NALM6 cells, experiment 2

description:
0898_001_NALM6m2_E01_MB_071207
Gene expression profile 6 hours ethanol treated NALM6 preB-ALL cells, experiment 2


title: 6 hours glucocorticoid treated NALM6 cells, experiment 1

description:
0897_001_NALM6p1_E01_MB_071207
Gene expression profile 6 hours glucocorticoid treated NALM6 preB-ALL cells, experiment 1


title: 6 hours glucocorticoid treated NALM6 cells, experiment 3

description:
0901_001_NALM6p3_E01_MB_071207
Gene expression profile 6 hours glucocorticoid treated NALM6 preB-ALL cells, experiment 3


title: 6 hours ethanol treated NALM6 cells, experiment 3

description:
0900_001_NALM6m3_E01_MB_071207
Gene expression profile 6 hours ethanol treated NALM6 preB-ALL cells, experiment 3


title: 6 hours ethanol treated NALM6 cells, experiment 1

description:
0896_001_NALM6m1_E01_MB_071207
Gene expression profile 6 hours ethanol treated NALM6 preB-ALL cells, experiment 1


title: 2 hours glucocorticoid treated NALM6 cells, experiment 3

description:
0914_001_NALM2p3_E01_MB_191207
Gene expression profile 2 hours glucocorticoid treated NALM6 preB-ALL cells, experiment 3


title: 2 hours ethanol treated NALM6 cells, experiment 3

description:
0913_001_NALM2m3_E01_MB_191207
Gene expression profile 2 hours ethanol treated NALM6 preB-ALL cells, experiment 3


description:
0919_001_2hpluIgG_P01_SJ_220108
2 hours glucocorticoid treated NALM6 cells, ChIP using antibody against IgG, experiment 1

hyb_protocol: Target samples were hybridized to Affymetrix Human Promoter 1.0R Tiling microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

data_processing: The CEL files were directly read by the ReadAffy function from Bioconductor's affy package that reads the full CEL file.  Raw data was background adjusted using the GCRMA method (option GSB.adjust set to FALSE) and subsequently quantiles normalized.

source_name: NALM6 preB-ALL cell line

label_protocol: Targets were labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: Precursor B-ALL NALM6 cells were cultured in RPMI 1640 supplemented with 10% fetal calf serum and 2mM L-glutamine at 37C, 5% carbon-dioxide and saturated humidity.

extract_protocol: DNA extracted from immunoprecipitated chromatin samples was processed according to the manufacturer's protocols.

value: anti-IgG [normal rabbit IgG]

tag: chip antibody vendor

value: Santa Cruz


description:
0925_001_2hminIgG_P01_SJ_240108
2 hours ethanol treated NALM6 cells, ChIP using antibody against IgG, experiment 3


description:
0813_001_2hpluGR_P01_SJ_070807
2 hours glucocorticoid treated CEM-C7H2 cells, ChIP using antibody against GR, experiment 1

source_name: CCRF-CEM-C7H2 T-ALL cell line

growth_protocol: T-ALL CCRF-CEM-C7H2 cells were cultured in RPMI 1640 supplemented with 10% fetal calf serum and 2mM L-glutamine at 37C, 5% carbon-dioxide and saturated humidity.

value: CCRF-CEM-C7H2 T-ALL

value: anti GR [GR (H-300) X (rabbit polyclonal)]


description:
0817_001_2hpluGR_P01_SJ_070807
2 hours glucocorticoid treated CEM-C7H2 cells, ChIP using antibody against GR, experiment 2


description:
0923_001_2hpluIgG_P01_SJ_230108
2 hours glucocorticoid treated NALM6 cells, ChIP using antibody against IgG, experiment 2


description:
0922_001_2hminGR_P01_SJ_230108
2 hours ethanol treated NALM6 cells, ChIP using antibody against GR, experiment 2


title: 2 hours glucocorticoid treated NALM6 cells, experiment 2

description:
0912_001_NALM2p2_E01_MB_191207
Gene expression profile 2 hours glucocorticoid treated NALM6 preB-ALL cells, experiment 2


description:
0818_001_2hminIgG_P01_SJ_090807
2 hours ethanol treated CEM-C7H2 cells, ChIP using antibody against IgG, experiment 3


description:
0917_001_2hminIgG_P01_SJ_220108
2 hours ethanol treated NALM6 cells, ChIP using antibody against IgG, experiment 1


description:
0819_001_2hminGR_P01_SJ_090807
2 hours ethanol treated CEM-C7H2 cells, ChIP using antibody against GR, experiment 3


title: 2 hours ethanol treated NALM6 cells, experiment 2

description:
0911_001_NALM2m2_E01_MB_191207
Gene expression profile 2 hours ethanol treated NALM6 preB-ALL cells, experiment 2


description:
0928_001_2hpluGR_P01_SJ_240108
2 hours glucocorticoid treated NALM6 cells, ChIP using antibody against GR, experiment 3


description:
0811_001_2hminGR_P01_SJ_070807
2 hours ethanol treated CEM-C7H2 cells, ChIP using antibody against GR, experiment 1


description:
0812_001_2hpluIgG_P01_SJ_070807
2 hours glucocorticoid treated CEM-C7H2 cells, ChIP using antibody against IgG, experiment 1


title: 2 hours ethanol treated NALM6 cells, experiment 1

description:
0909_001_NALM2m1_E01_MB_191207
Gene expression profile of 2 hours ethanol treated NALM6 preB-ALL cells, experiment 1


description:
0815_001_2hminGR_P01_SJ_070807
2 hours ethanol treated CEM-C7H2 cells, ChIP using antibody against GR, experiment 2


description:
0821_001_2hpluGR_P01_SJ_090807
2 hours glucocorticoid treated CEM-C7H2 cells, ChIP using antibody against GR, experiment 3


description:
0924_001_2hpluGR_P01_SJ_230108
2 hours glucocorticoid treated NALM6 cells, ChIP using antibody against GR, experiment 2


description:
0918_001_2hminGR_P01_SJ_220108
2 hours ethanol treated NALM6 cells, ChIP using antibody against GR, experiment 1


description:
0814_001_2hminIgG_P01_SJ_070807
2 hours ethanol treated CEM-C7H2 cells, ChIP using antibody against IgG, experiment 2


description:
0810_001_2hminIgG_P01_SJ_070807
2 hours ethanol treated CEM-C7H2 cells, ChIP using antibody against IgG, experiment 1


description:
0921_001_2hminIgG_P01_SJ_230108
2 hours ethanol treated NALM6 cells, ChIP using antibody against IgG, experiment 2


description:
0816_001_2hpluIgG_P01_SJ_070807
2 hours glucocorticoid treated CEM-C7H2 cells, ChIP using antibody against IgG, experiment 2


description:
0926_001_2hminGR_P01_SJ_240108
2 hours ethanol treated NALM6 cells, ChIP using antibody against GR, experiment 3


description:
0920_001_2hpluGR_P01_SJ_220108
2 hours glucocorticoid treated NALM6 cells, ChIP using antibody against GR, experiment 1


title: 2 hours glucocorticoid treated NALM6 cells, experiment 1

description:
0910_001_NALM2p1_E01_MB_191207
Gene expression profile 2 hours glucocorticoid treated NALM6 preB-ALL cells, experiment 1


description:
0820_001_2hpluIgG_P01_SJ_090807
2 hours glucocorticoid treated CEM-C7H2 cells, ChIP using antibody against IgG, experiment 3


description:
0927_001_2hpluIgG_P01_SJ_240108
2 hours glucocorticoid treated NALM6 cells, ChIP using antibody against IgG, experiment 3


description:
0490_001_C7H2-24-_E01_SJ_060706
Gene expression profile of 24 hours ethanol treated CEM-C7H2 cells, experiment 1


description:
0866_001_C7H2-6-p_E01_MB_121007
Gene expression profile of 6 hours glucocorticoid treated CEM-C7H2 cells, experiment 3


description:
0489_001_C7H2-6h+_E01_SJ_060706
Gene expression profile of 6 hours glucocorticoid treated CEM-C7H2 cells, experiment 1


description:
0495_001_C7H2-24+_E01_SJ_060706
Gene expression profile of 24 hours glucocorticoid treated CEM-C7H2 cells, experiment 3


description:
0492_001_C7H2-24-_E01_SJ_060706
Gene expression profile of 24 hours ethanol treated CEM-C7H2 cells, experiment 2


title: cR-/mR-

city: Matsumoto

first: Katsunori

last: Sasaki

state: Nagano

address: 3-1-1 Asahi

department: School of Medicine

country: Japan

institute: Shinsyu University

hyb_protocol: Aliquots (3μg) of cRNA were fragmented at 94℃ for 15 min and hybridized onto a ConPath  chip in the presence of formamide (final concentration 10% v⁄v) at 37℃ for 16 h.

scan_protocol: scanned using an Agilent Technologies Scanner at a resolution of 10 μm.Images were quantified using Agilent Feature Extraction Software (version

data_processing: Default Agilent Feature Extraction Software (version 9.1) settings

source_name: human ES cells

label_protocol: RNA was amplified using a MessageAmp  II-biotin Enhanced Single Round amplified RNA amplification kit (Ambion, Austin, TX, USA).

growth_protocol: The hES cells (KhES-1 supplied from Institute for Frontier Medical Science, Kyoto University, Japan)  were used according to the hES cell research guideline established by the Japanese government and were cultured on a feeder layer of MEF cells in DMEM/F12 (Nissui Pharmaceutical Co., Ibaraki, Japan) supplemented with 20% (vol/vol) Knockout Serum Replacement (KSR: Invitrogen, Carlsbad, CA, USA), 2mM L-glutamine (Invitrogen), 0.1mM nonessential amino acids (Invitrogen) and 0.1mM 2-mercaptoethanol (Sigma, St. Louis, MO USA) under 3% CO2. For routine passage, hES cell colonies were dispersed gently after treating them with 0.25% trypsin and 0.1mg/ml collagenase Ⅳ(Invitrogen) in PBS containing 20% KSR and 1mM CaCl2, which was developed by Suemori et al.  at 37℃ for 5 min, and pipetted gently with the medium. The clumps were seeded on the dish with the new feeder layer.

extract_protocol: To investigate effects of Rock inhibitor in dissociation and cryopreservation of hES cells on apoptosis-associated gene pathway, the following procedures were performed.   Total RNA from each samples in cR+/mR+, cR+/mR-, cR-/mR+ or cR-/mR- was extracted by using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: First, hES cell colonies were detached from the feeder layer with the above dispersion cocktail and partially dissociated as clumps.  Next, contaminated MEF cells were removed by incubating the cell suspension on a gelatin-coated plate at 37°C for 1hr in the culture medium, because of their rapid adhesion to it.  The remained hES cell clumps were separated from the suspension by centrifugation, incubated in 0.25% (vol/vol) trypsin-EDTA (invitrogen) at 37°C for 4 min, pipetted with the conditioned medium containing 10μM of Y-27632 or none, dissociated completely into single cells, centrifuged, diluted with the medium and then passed through Cell Strainer (pore size: 40μm, BD Falcon, New Jersey, USA).  Respectively the dissociated cells in the designed medium were centrifuged, diluted with 1ml of the freezing medium consisting of hES cell culture medium with 10% DMSO (Sigma-Aldrich Co.), transferred to the cryovials (NALGENE Cryogenic Vials, Nalge NUNC, NY, USA) were frozen slowly in a freezing container, BICELL (NIHON FREEZER, Tokyo, JAPAN) to -80°C overnight. The cooling rate of the BICELL was described by our previous report.  Then they were stored in liquid nitrogen more than one week and were rapidly thawed in a water bath at 37°C.

value: addition of 10μM of Y-27632 to no addition to any medium (cR-/mR-)


title: cR-/mR+

value: addition of 10μM of Y-27632 to only addition to post-thawing medium (cR-/mR+)


title: cR+/mR-

value: addition of 10μM of Y-27632 to only addition to cryoprotection (cR+/mR-)


title: cR+/mR+

value: addition of 10μM of Y-27632 to cryoprotection solution and post-thawing medium (cR+/mR+)


description:
0491_001_C7H2-24+_E01_SJ_060706
Gene expression profile of 24 hours glucocorticoid treated CEM-C7H2 cells, experiment 1


description:
0735_001_C7H2-2p_E01_SJ_070607
Gene expression profile of 2 hours glucocorticoid treated CEM-C7H2 cells, experiment III


description:
0737_001_C7H2-2p_E01_SJ_070607
Gene expression profile of 2 hours glucocorticoid treated CEM-C7H2 cells, experiment IV


description:
0409_001_C7H2-2ug_E01_SJ_160306
Gene expression profile of 6 hours glucocorticoid treated CEM-C7H2 cells, experiment 0


description:
0738_001_C7H2-2m_E01_SJ_070607
Gene expression profile of 2 hours ethanol treated CEM-C7H2 cells, experiment V


description:
0734_001_C7H2-2m_E01_SJ_070607
Gene expression profile of 2 hours ethanol treated CEM-C7H2 cells, experiment III


description:
0741_001_C7H2-05p_E01_MB_150607
Gene expression profile of 30 minutes glucocorticoid treated CEM-C7H2 cells, experiment III


description:
0488_001_C7H2-6h-_E01_SJ_060706
Gene expression profile of 6 hours ethanol treated CEM-C7H2 cells, experiment 1


description:
0743_001_C7H2-05p_E01_MB_150607
Gene expression profile of 30 minutes glucocorticoid treated CEM-C7H2 cells, experiment IV


description:
0739_001_C7H2-2p_E01_SJ_070607
Gene expression profile of 2 hours glucocorticoid treated CEM-C7H2 cells, experiment V


description:
0744_001_C7H2-05m_E01_MB_150607
Gene expression profile of 30 minutes ethanol treated CEM-C7H2 cells, experiment V


description:
0493_001_C7H2-24+_E01_SJ_060706
Gene expression profile of 24 hours glucocorticoid treated CEM-C7H2 cells, experiment 2


description:
0736_001_C7H2-2m_E01_SJ_070607
Gene expression profile of 2 hours ethanol treated CEM-C7H2 cells, experiment IV


description:
0865_001_C7H2-6-m_E01_MB_121007
Gene expression profile of 6 hours ethanol treated CEM-C7H2 cells, experiment 3


title: Rhesus Siv+Meth,Caudate biological rep2

city: Omaha

first: Gurudutt

last: Pendyala

state: NE

address: 985800 Nebraska Medical Center

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

description:
Gene expression data from 19 weeks SIV infection+23 weeks METH
Guru 554 Rhesus 1-9-09.CEL

hyb_protocol: Following fragmentation, 200 ng of cRNA were hybridized for 16 hr at 42C on Affymetrix Rhesus Macaque Genome Array. GeneChips were washed and stained in the Affymetrix Gene chip system.

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

data_processing: The data were analyzed using the Partek Genomics Suite and probe sets mapped to genes using the database for annotation.

organism: Macaca mulatta

source_name: Rhesus Brain

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

growth_protocol: Not Applicable

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

treatment_protocol: Six Rhesus monkeys were chronically infected with SIVmac251 for 19 weeks followed by an escalating dose regimen of METH for 23 weeks. Control monkeys received Saline injections on the same schedule.

value: Caudate

tag: infection

value: SIV

tag: agent

value: METH

tag: protocol

value: 19 weeks SIV infection+23 weeks METH


title: Rhesus Siv+Meth,Caudate biological rep3

description:
Gene expression data from 19 weeks SIV infection+23 weeks METH
Guru 555 Rhesus 1-9-09.CEL


description:
0494_001_C7H2-24-_E01_SJ_060706
Gene expression profile of 24 hours ethanol treated CEM-C7H2 cells, experiment 3


title: Rhesus Siv+Meth,Caudate biological rep1

description:
Gene expression data from 19 weeks SIV infection+23 weeks METH
Guru 542 Rhesus 1-9-09.CEL


title: Rhesus Ctrl,Caudate biological rep2

description:
Gene expression data from 19 weeks SIV infection+23 weeks Saline
Guru 518 Rhesus 1-9-09_2.CEL

value: PBS

value: 19 weeks SIV infection+23 weeks Saline


description:
0745_001_C7H2-05p_E01_MB_150607
Gene expression profile of 30 minutes glucocorticoid treated CEM-C7H2 cells, experiment V


description:
0740_001_C7H2-05m_E01_MB_150607
Gene expression profile of 30 minutes ethanol treated CEM-C7H2 cells, experiment III


description:
0742_001_C7H2-05m_E01_MB_150607
Gene expression profile of 30 minutes ethanol treated CEM-C7H2 cells, experiment IV


title: Rhesus Siv+Meth,Hippo biological rep1

description:
Gene expression data from 19 weeks SIV infection+23 weeks METH
Guru 542 Rhesus 4-3-09.CEL

value: Hippocampus


title: jejunum_ B10A_ 1_ GF GF-uMT2green

city: Bethesda

first: Natalia

last: Shulzhenko

state: MD

address: 9000 Rockville Pike

department: Laboratory of Cellular and Molecular Immunology

institute: NIAID, USA

description: full-thickness 2 cm of jejunum from the middle of small intestine

hyb_protocol: Corresponding experimental (knock-out) and control samples were co-hybridized using MAUI hybridization system as described by Schaupp et al. 2005; PMID: 15679093

scan_protocol: Images were scanned by GenePix4000B Scanner (Axon Instruments/Molecular Devices).

data_processing: After subtraction of local background, signal intensity values were filtered to remove those lower than 10 and median normalized using BRB Array Tools.

organism: Mus musculus

source_name: jejunum

label_protocol: 20 ug of total RNA were directly fluorescently labeled in a reverse transcription reaction using Cy3-dUTP or Cy5-dUTP (GE Healthcare) and Oligo(dT)12-18 Primer and SuperScript II reverse transcriptase

growth_protocol: tissues and cells  were isolated from mice: B220+ B lymphocytes were isolated from spleen;  2 cm of full-thickness jejunum from the middle of small intestine was dissected

extract_protocol: tissues were homogenized in Trizol or RLT buffer from Qiagen RNAeasy KIT. Total RNA were isolated according to standard protocol

tag: gender (sex)

value: M

tag: genotype (0=ko;1=control)

tag: strain

tag: germ status (gf=germ-free)

value: GF

tag: mutation

value: no mut

tag: tissue type

value: jejunum

tag: array name


description:
0407_001_C7H2-2ug_E01_SJ_160306
Gene expression profile of 6 hours ethanol treated CEM-C7H2 cells, experiment 0

tag: cell line

value: CCRF-CEM-C7H2 T-ALL

value: ethanol


title: jejunum_ B6_ 0_ GF GF-Jh8green

value: JH


title: Rhesus Ctrl,Caudate biological rep1

description:
Gene expression data from 19 weeks SIV infection+23 weeks Saline
Guru 514 Rhesus 1-9-09.CEL

tag: tissue


title: Rhesus Siv+Meth,Hippo biological rep3

description:
Gene expression data from 19 weeks SIV infection+23 weeks METH
Guru 555 Rhesus 4-3-09.CEL


title: jejunum_ B10A_ 0_ GF GF-uMT3red

value: uMT


title: Rhesus Ctrl,Hippo biological rep1

description:
Gene expression data from 19 weeks SIV infection+23 weeks Saline
Guru 514 Rhesus 4-3-09.CEL


title: jejunum_ B6_ 0_ GF GF-Jh4green


title: Rhesus Ctrl, Hippo biological rep2

description:
Gene expression data from 19 weeks SIV infection+23 weeks Saline
Guru 518 Rhesus 4-3-09_2.CEL


title: Rhesus Ctrl,Caudate biological rep3

description:
Gene expression data from 19 weeks SIV infection+23 weeks Saline
Guru 519 Rhesus 1-9-09.CEL


title: jejunum_ B10A_ 0_ GF GF-uMT2red


title: jejunum_ B6_ 1_ GF GF-Jh7red

value: F


title: jejunum_ B10A_ 1_ GF GF-uMT1green


title: jejunum_ B10A_ 1_ GF GF-uMT3green


title: jejunum_ B6_ 1_ GF GF-Jh4red


title: jejunum_ B6_ 0_ GF GF-Jh7green


title: jejunum_ B10A_ 0_ GF GF-uMT1red


title: Rhesus Ctrl,Hippo biological rep3

description:
Gene expression data from 19 weeks SIV infection+23 weeks Saline
Guru 519 Rhesus 4-3-09.CEL


title: jejunum_ B6_ 1_ GF GF-Jh6green


title: Rhesus Siv+Meth,Hippo biological rep2

description:
Gene expression data from 19 weeks SIV infection+23 weeks METH
Guru 554 Rhesus 4-3-09.CEL


title: jejunum_ B6_ 0_ GF GF-Jh6red


title: jejunum_ B6_ 0_ GF GF-Jh5red


title: jejunum_ B6_ 1_ GF GF-Jh8red


title: jejunum_ B6_ 1_ GF GF-Jh5green


title: jejunum_ B6_ 1_ GF GF-Jh2red


title: jejunum_ B6_ 0_ GF GF-Jh2green


title: jejunum_ B6_ 0_ GF GF-Jh3red


title: jejunum_ B6_ 1_ GF GF-Jh3green


title: B lymphocytes_ balbc_ 1_ non-GF 87616BC

description: B220 pos cells isolated from spleen

source_name: B lymphocytes

value: balbc

value: non-GF

tag: cell type

value: B lymphocytes


title: jejunum_ B6_ 1_ GF GF-Jh1red


title: B lymphocytes_ balbc_ 1_ non-GF 87617BC

description: B220 pos cells isolated from spleen


title: jejunum_ B6_ 0_ GF GF-Jh1green


title: B lymphocytes_ balbc_ 1_ non-GF 87615BC

description: B220 pos cells isolated from spleen


title: B lymphocytes_ balbc_ 1_ non-GF 87605BC

description: B220 pos cells isolated from spleen


title: jejunum_ B10A_ 1_ non-GF 85228G


title: B lymphocytes_ balbc_ 1_ non-GF 87613BC

description: B220 pos cells isolated from spleen


title: jejunum_ balbc_ 0_ non-GF 87383G


title: B lymphocytes_ B10A_ 1_ non-GF 86100BC

description: B220 pos cells isolated from spleen


title: jejunum_ balbc_ 1_ non-GF 87365G


title: B lymphocytes_ balbc_ 1_ non-GF 87612BC

description: B220 pos cells isolated from spleen


title: jejunum_ B10A_ 0_ non-GF 85229G


title: jejunum_ balbc_ 1_ non-GF 87381G


title: B lymphocytes_ balbc_ 1_ non-GF 87614BC

description: B220 pos cells isolated from spleen


title: jejunum_ B10A_ 0_ non-GF 86097G


title: B lymphocytes_ B10A_ 1_ non-GF 86098BC

description: B220 pos cells isolated from spleen


title: jejunum_ balbc_ 1_ non-GF 87379G


title: jejunum_ balbc_ 0_ non-GF 87380G


title: B lymphocytes_ B10A_ 1_ non-GF 86101BC

description: B220 pos cells isolated from spleen


title: jejunum_ balbc_ 1_ non-GF 87386G


title: jejunum_ B10A_ 0_ non-GF 85227G


title: jejunum_ balbc_ 1_ non-GF 87385G


title: jejunum_ B10A_ 1_ non-GF 85226G


title: jejunum_ balbc_ 0_ non-GF 87367G


title: jejunum_ B10A_ 1_ non-GF 85225G


title: jejunum_ balbc_ 0_ non-GF 87387G


title: jejunum_ B10A_ 0_ non-GF 86101G


title: jejunum_ balbc_ 0_ non-GF 87364G


title: jejunum_ B10A_ 1_ non-GF 86096G


title: B lymphocytes_ balbc_ 1_ non-GF 87604BC

description: B220 pos cells isolated from spleen


title: B lymphocytes_ B10A_ 1_ non-GF 85224BC

description: B220 pos cells isolated from spleen


title: B lymphocytes_ B10A_ 1_ non-GF 85225BC

description: B220 pos cells isolated from spleen


title: B lymphocytes_ B10A_ 1_ non-GF 85222BC

description: B220 pos cells isolated from spleen


title: jejunum_ balbc_ 0_ non-GF 85216G


title: jejunum_ B10A_ 1_ non-GF 85222G


title: jejunum_ B10A_ 1_ non-GF 85215G


title: B lymphocytes_ B10A_ 1_ non-GF 85221BC

description: B220 pos cells isolated from spleen


title: jejunum_ B10A_ 1_ non-GF 85213G


title: jejunum_ B10A_ 0_ non-GF 85214G


title: jejunum_ B10A_ 1_ non-GF 85218G


title: jejunum_ B10A_ 1_ non-GF 84103G


title: jejunum_ B10A_ 0_ non-GF 85212G


title: jejunum_ B10A_ 1_ non-GF 85210G


title: jejunum_ B10A_ 0_ non-GF 84102G


title: jejunum_ balbc_ 0_ non-GF 87385


title: jejunum_ balbc_ 0_ non-GF 87365


title: jejunum_ B10A_ 0_ non-GF 85220G


title: jejunum_ B10A_ 1_ non-GF 84100G


title: jejunum_ balbc_ 0_ non-GF 87379


title: jejunum_ balbc_ 0_ non-GF 87386


title: jejunum_ B10A_ 0_ non-GF 84101G


title: jejunum_ balbc_ 1_ non-GF 87364


title: jejunum_ balbc_ 0_ non-GF 87381


title: jejunum_ B10A_ 0_ non-GF 86096


title: jejunum_ B10A_ 1_ non-GF 86097


title: jejunum_ B10A_ 0_ non-GF 86100


title: jejunum_ balbc_ 1_ non-GF 87383


title: jejunum_ balbc_ 1_ non-GF 87380


title: jejunum_ B10A_ 1_ non-GF 85229


title: jejunum_ balbc_ 1_ non-GF 87387


title: jejunum_ B10A_ 0_ non-GF 86098


title: jejunum_ balbc_ 1_ non-GF 87367


title: jejunum_ B10A_ 1_ non-GF 85227


title: jejunum_ B10A_ 0_ non-GF 85226


title: jejunum_ B10A_ 1_ non-GF 85221


title: jejunum_ B10A_ 0_ non-GF 85228


title: jejunum_ B10A_ 0_ non-GF 85218


title: jejunum_ B10A_ 1_ non-GF 85224


title: jejunum_ B10A_ 1_ non-GF 85220


title: jejunum_ B10A_ 1_ non-GF 85216


title: jejunum_ B10A_ 0_ non-GF 85215


title: jejunum_ B10A_ 1_ non-GF 85212


title: jejunum_ B10A_ 0_ non-GF 85213


title: jejunum_ B10A_ 1_ non-GF 84101


title: jejunum_ B10A_ 1_ non-GF 84102


title: jejunum_ B10A_ 1_ non-GF 85214


title: jejunum_ B10A_ 0_ non-GF 84103


title: jejunum_ B10A_ 0_ non-GF 85210


title: Nrl-KO at 10 months-3

city: Rockville

first: Radu

last: Cojocaru

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

description: Ribosome reduced total RNA

hyb_protocol: Following fragmentation and labelling, 5.5 ug of cDNA were hybridized at 45C for 18 hours.  GeneChips were washed and stained in the Affymetrix FS450.

scan_protocol: GeneChips were scanned with an Affymetrix GCS3000 7G

data_processing: I used GeneSpring for analysis. I made a 'core level' analysis and did RMA for normalization. I used quantile normalization with log probes base 2 and for probeset normalization I did median polish.

source_name: Nrl-KO at 10 months

label_protocol: Amplified sense strand cDNA was generated using the GeneChip Whole  Transcript Sense Target Labeling Assay Kit (Affymetrix).

extract_protocol: RNA was extracted using RNeasy with on-column DNase treatment (Qiagen).  Ribosomal RNA was reduced from one microgram of total RNA using RiboMinus Transcriptome Isolation Kit (Human/Mouse) (Invitrogen).

value: Retina

tag: genotype

value: Nrl-/-

tag: age

value: 10 month


title: Nrl-KO at 10 months-4

description: Ribosome reduced total RNA


title: Nrl-KO at 2 months-2

description: Ribosome reduced total RNA

source_name: Nrl-KO at 2 months

value: 2 month


title: Nrl-KO at 2 months-4

description: Ribosome reduced total RNA


title: Nrl-KO at 2 months-3

description: Ribosome reduced total RNA


title: Nrl-KO at 10 months-2

description: Ribosome reduced total RNA


title: Nrl-KO at 10 months-1

description: Ribosome reduced total RNA


title: jejunum_ B10A_ 0_ non-GF 84100


title: Nrl-KO at 4 months-2

description: Ribosome reduced total RNA

source_name: Nrl-KO at 4 months

value: 4 month


title: Nrl-KO at 4 months-1

description: Ribosome reduced total RNA


title: Nrl-KO at 1month-4

description: Ribosome reduced total RNA

source_name: Nrl-KO at 1month

value: 1 month


title: Nrl-KO at 2 months-1

description: Ribosome reduced total RNA


title: Nrl-KO at 1month-3

description: Ribosome reduced total RNA


title: Nrl-KO at 4 months-3

description: Ribosome reduced total RNA


title: Nrl-KO at 6 months-2

description: Ribosome reduced total RNA

source_name: Nrl-KO at 6 months

value: 6 month


title: Nrl-KO at 1month-2

description: Ribosome reduced total RNA


title: Nrl-KO at 6 months-4

description: Ribosome reduced total RNA


title: Nrl-KO at 6 months-1

description: Ribosome reduced total RNA


title: Nrl-KO at 6 months-3

description: Ribosome reduced total RNA


title: Nrl-KO at 4 months-4

description: Ribosome reduced total RNA


title: G119_biopsy_gastric_normal

city: Seoul

first: Dong Yoon

last: Park

address: 134 Shinchon-dong, Seodaemun-gu

department: Biochemistry

country: South Korea

institute: Yonsei University

description: Raw data file: T00338643.txt

hyb_protocol: For the hybridization of each slide, 10 ug of fragmented target cRNA was used in 260 ul of hybridization buffer. The hybridization buffer was heated at 90°C for 5 minutes to denature the cRNA, and chilled on ice for 5 minutes. The sample was vortexed for 5 seconds at maximum speed, and 250 ul was injected into the inlet port of hybridization chamber, placed in a 12-slide shaker tray. The hybridization chamber ports were sealed with 1 cm sealing strips, and the shaker tray containing the slides was loaded into a shaking incubator. The slides were incubated for 18 hours at 37°C with shaking at 300 rpm.

scan_protocol: The processed slides were scanned with GenePix 4000B (Molecular Devices, USA) to produce Tiff image files with following setting: laser wave length 635 nm, the photomultiplier tube (PMT) voltage 600, and scan resolution 10 um.

data_processing:
The image files were quantified with Codelink Expression Analysis v4.0 (GE healthcare, USA), and data were normalized using recommended default option.  The final result was transformed into GeneSpring GX compatible format.
In Codelink data file, there's a column named "GENESPRINGFLAG", which has one of three data values: P(present), M(marginal), A(absent). I included only P & M flag spot data in matrix datasheet, so any spot with A flag is represented as "null" in the data table below.

source_name: gastric tissue, normal

label_protocol: For post-hybridization dye coupling process, the slide holder was removed from the shaking incubator before the hybridization chamber was removed off each slide. The slide was briefly rinsed in 0.75 x TNT buffer (0.075 M Tris-HCl pH 7.6, 0.1125 M NaCl, and 0.0375% Tween 20) at room temperature, and washed in 0.75 x TNT buffer at 42°C for 60 minutes. The signal was developed using a 1:500 dilution of Cy5-streptavidin (GE Healthcare, USA) for 30 minutes at room temperature (dye coupling step). The excess dye was washed off 4 times with 1 x TNT buffer (0.1 M Tris-HCl pH 7.6, 0.15 M NaCl, and 0.05% Tween 20) for 5 minutes each step at room temperature. The slides was briefly rinsed with final washing buffer (0.1 x SSC and 0.05% Tween 20) and dried by applying centrifugal force gently (approximately 800 rpm) for 5 minutes for the following scanning process.

extract_protocol: Total RNA was extracted with TRIzol Reagent (Invitrogen, USA, Cat. No. 15596-018) according to the manufacturer’s recommended protocol. 2 µg of total RNA were added to a reaction mix in a final volume of 12 µl, containing T7-(dT)24 oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. With the mixture remaining on ice, 2 µl of 10x first-strand buffer, 4 µl of 5 mM dNTP mix, 1 ul of RNase inhibitor(40U/ul) and 1 µl of SuperscriptTM II RNase H– reverse transcriptase (200 U/µl) was added to make a final volume of 20 µl, and the mixture incubated for 2 h in a 42°C water bath. Second-strand cDNA was synthesized in a final volume of 100 µl, in a mixture containing 10 µl of 10x second-strand buffer, 4 µl of 5 mM dNTP mix, 2 µl of DNA polymerase mix (20 U/µl) and 1 µl of RNase H (2 U/µl) for 2 h at 16°C. The cDNA was purified using a Qiagen QIAquick purification kit, dried down, and resuspended in IVT reaction mix in a final volume of 40 ul, containing 4 µl of 10x reaction buffer, 4 µl of 75 mM ATP, 4 µl of 75 mM GTP, 4 µl of 75 mM CTP, 3 µl of 75 mM UTP, 7.5 µl of 10 mM Biotin 11-UTP and 4 µl enzyme mix. The reaction mix was incubated for 14 h at 37°C and cRNA target purified using an RNeasy® kit (Qiagen). cRNA yield was quantified by measuring the UV absorbance at 260 nm, and fragmented in 40 mM Tris–acetate (TrisOAc) pH 7.9, 100 mM KOAc and 31.5 mM MgOAc, at 94°C for 20 min. This resulted typically in a fragmented target with a size range between 100 and 200 bases.

value: gastric tissue

tag: disease state

value: normal


title: Nrl-KO at 1month-1

description: Ribosome reduced total RNA


title: G102_biopsy_gastric_normal

description: Raw data file: T00338287.txt


title: G146_biopsy_gastric_normal

description: Raw data file: T00338350.txt


title: G159_biopsy_gastric_normal

description: Raw data file: T00338288.txt


title: G116_biopsy_gastric_normal

description: Raw data file: T00338640.txt


title: G98_biopsy_gastric_normal

description: Raw data file: T00338642.txt


title: G157_biopsy_gastric_normal

description: Raw data file: T00338351.txt


title: G109_biopsy_gastric_normal

description: Raw data file: T00338286.txt


title: G118_biopsy_gastric_normal

description: Raw data file: T00338284.txt


title: G158_biopsy_gastric_normal

description: Raw data file: T00338349.txt


title: G164_biopsy_gastric_normal

description: Raw data file: T00338283.txt


title: G36_biopsy_gastric_tumor

description: Raw data file: T00322322.txt

source_name: gastric tissue, tumor

tag: Sex

value: tumor


title: G37_biopsy_gastric_tumor

description: Raw data file: T00322320.txt


title: G33_biopsy_gastric_tumor

description: Raw data file: T00322321.txt

value: M


title: G72_biopsy_gastric_tumor

description: Raw data file: T00321470.txt


title: 613_biopsy_gastric_tumor

description: Raw data file: T00321464.txt


title: G154_biopsy_gastric_tumor

description: Raw data file: T00321465.txt


title: G155_biopsy_gastric_tumor

description: Raw data file: T00321467.txt


title: G20_biopsy_gastric_tumor

description: Raw data file: T00321461.txt


title: G26_biopsy_gastric_tumor

description: Raw data file: T00321453.txt


title: c elegans_h2s_48h

city: Seattle

first: Dana

middle: L

last: Miller

state: WA

institute: University of Washington

description:
changes in expression after 48h exposure to 50 ppm H2S
reference raw data file 1: one_HA_231209_532.pair
reference raw data file 2: one_HAA_233075_532.pair
reference raw data file 3: one_HAB_232006_532.pair
experimental raw data file 1: two_48h_232006_532.pair
experimental raw data file 2: two_48h_233069_532.pair
experimental raw data file 3: two_48h_233075_532.pair

hyb_protocol: Hybridization was performed by the DNA Array Facility at the Fred Hutchinson Cancer Research Center following protocol provided by Nimblegen

scan_protocol: Scanning was performed by the DNA Array Facility at the Fred Hutchinson Cancer Research Center following protocol provided by Nimblegen

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, version 2.4.27 (Roche NimbleGen, Inc.). Data was filtered, keeping those genes with average intensity of >= 100 in at least one group and gene-wise stdev across all samples >shorth value using genefilter (Bioconductor release 2.4). Treated samples were paired with matched control to calculate M and A values, which were then used to loess normalize each array. Expression ratios (logFC) were determined using limma.
The 5 reference (untreated, ch2) pair files (one_HAA_233075_532.pair, one_HAA_319922_532.pair, one_HAB_232006_532.pair, one_HA_231209_532.pair, and one_HA_326249_532.pair) are available as a TAR archive at the foot of the Series record (reference_pair_files.tar). The raw data file associations are provided in the Sample 'description' field above.

organism: Caenorhabditis elegans

source_name: C. elegans N2 wild-type exposed to h2s for 48 h

label_protocol: Labeling was performed by the DNA Array Facility at the Fred Hutchinson Cancer Research Center following protocol provided by Nimblegen

growth_protocol: C. elegans were synchronized as starved first-stage larvae, then grown on NGM plates seeded with OP50 for 48 h. Total RNA was isoalted from first-day young adults

extract_protocol: total RNA was extracted using Trizol method followed by isopropanol precipitation

treatment_protocol: Animals were exposed to 50 ppm hydrogen sulfide in the gas phase for 1h, 12h, or 48 h. Gene expression was compared to controls not exposed to sulfide.

value: N2 Bristol

tag: h exposure to hydrogen sulfide

source_name: C. elegans N2 wild-type untreated


title: G28_biopsy_gastric_tumor

description: Raw data file: T00321451.txt


title: G120_biopsy_gastric_normal

description: Raw data file: T00338282.txt


title: G31_biopsy_gastric_tumor

description: Raw data file: T00321450.txt


title: c elegans_h2s_12h

description:
changes in expression after 12h exposure to 50 ppm H2S
reference raw data file 1: one_HA_231209_532.pair
reference raw data file 2: one_HAA_233075_532.pair
reference raw data file 3: one_HAB_232006_532.pair
experimental raw data file 1: six_12h_231184_532.pair
experimental raw data file 2: six_12h_233069_532.pair
experimental raw data file 3: six_12h_233075_532.pair

source_name: C. elegans N2 wild-type exposed to h2s for 12 h


title: c elegans_h2s_1h

description:
changes in expression after 1h exposure to 50 ppm H2S
reference raw data file 1: one_HAB_232006_532.pair
reference raw data file 2: one_HAA_319922_532.pair
reference raw data file 3: one_HA_326249_532.pair
experimental raw data file 1: three_1h_231209_532.pair
experimental raw data file 2: three_1h_319898_532.pair
experimental raw data file 3: three_1h_326249_532.pair

source_name: C. elegans N2 wild-type exposed to h2s for 1 h


title: G23_biopsy_gastric_tumor

description: Raw data file: T00321435.txt


title: G25_biopsy_gastric_tumor

description: Raw data file: T00321432.txt


title: G24_biopsy_gastric_tumor

description: Raw data file: T00321434.txt


title: G68_biopsy_gastric_tumor

description: Raw data file: T00321469.txt


title: Normal-LB22

city: Ithaca

first: Wei

last: Wang

state: NY

address: T2-003 Vet Res Tower

institute: Cornell University

description: Affymetrix

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Affymetrix GCOS

organism: Gallus gallus

source_name: ovary

label_protocol: Ambion MessageAmp Biotin Enhanced kit

extract_protocol: Trizol

value: ovary

value: Normal


title: G22_biopsy_gastric_tumor

description: Raw data file: T00321436.txt


title: G113_biopsy_gastric_tumor

description: Raw data file: T00288185.txt

value: F


title: 611_biopsy_gastric_tumor

description: Raw data file: T00321463.txt


title: SC536_biopsy_gastric_tumor

description: Raw data file: T00280633.txt


title: G27_biopsy_gastric_tumor

description: Raw data file: T00321452.txt


title: G35_biopsy_gastric_tumor

description: Raw data file: T00321437.txt


title: G34_biopsy_gastric_tumor

description: Raw data file: T00321433.txt


title: SC538_biopsy_gastric_tumor

description: Raw data file: T00288168.txt


title: Cancer-LB11

description: Affymetrix

value: cancer


title: SC520_biopsy_gastric_tumor

description: Raw data file: T00280631.txt


title: SC519_biopsy_gastric_tumor

description: Raw data file: T00280630.txt


title: SC540_biopsy_gastric_tumor

description: Raw data file: T00288170.txt


title: Mutant DPD25 time4 rep2

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

country: China

institute: Huazhong Agricultural University

description: Two biological repetitions were combined

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit (Agilent). 1μg of cRNA were mixed with blocking agent, fragmentation buffer and incubated at 60°C for 30 min for fragmentation. GEx Hybridization Buffer were added and 100 μl mixture were hybridized at 65°C for 17 hours with 10 rpm rotation. The arrays were washed two times using wash buffer 1 and 2 from Gene Expression Wash Buffer Kit (Agilent).

scan_protocol: Arrays were scanned using Agilent Microarray Scanner System G2565BA (Agilent) with resolution of 5μm. The scanner uses 100% and 10% PTM respectively and combines the two data automatically.

data_processing: We used and submitted only one probe signal (the probe that near the 3 end of the gene) for each gene in this study. The 2477 rows in the sample data table represented 2477 ORFs on the array. The data were analyzed using Feature Extraction Software (Agilent). The signal intensity were log2 normalized.

organism: Actinobacillus pleuropneumoniae

source_name: Mutant

label_protocol: cDNA were transcribed into cRNA using T7 RNA Polymerase and aaUTP (Ambion). cRNA were purified using QIAGEN RNeasy Mini kit (QIAGEN). 4μg cRNA were combined with DMSO and 0.3M NaHCO3 and then were added into Cy3 NHS ester (GE healthcare). The mixture were incubated at 25°C for 1 hour. 4M Hydroxylamine were added and incubated at 25°C for 15min. The labeled cRNA were purified using QIAGEN RNeasy Mini kit (QIAGEN).

growth_protocol: A. pleuropneumoniae strains were cultured in TSB medium supplemented with 10 μg/ml of nicotinamide adenine dinucleotide (NAD) and 10% (v/v) filtered cattle serum at 37°C. For samples from the mutant complemented with DPD, 100μM and 25μM DPD were added into the medium before early exponential phase as well as one hour before late exponential phase respectively. The samples were collected from early, middle, late exponential phase and stationary phase respectively and the total RNA were extracted using Trizol reagent according to the manufacturer’s instructions.

extract_protocol: RNA were extracted using RNA-Solv Reagent (Omega) according to the manufacturer’s instructions. Total RNA were purified using QIAGEN RNeasy Mini Kit (QIAGEN). 2μg RNA were reverse-transcribed into cDNA using T7 promotor primer.

treatment_protocol: cultured in TSB medium supplemented with 25μM DPD to stationary phase

tag: genotype variation

value: luxS negative


title: Mutant DPD25 time4 rep1


title: Normal-LB3

description: Affymetrix


title: Mutant DPD25 time3 rep2

treatment_protocol: cultured in TSB medium supplemented with 25μM DPD to late exponential phase


title: Mutant DPD25 time3 rep1


title: PPNAD 3

first: Madson

middle: Q

last: Almeida

address: 10 Center Drive, MSC 1103

department: Section on Genetics and Endocrinology / NICHD

institute: NIH

description: replicate 1

scan_protocol: Standard Illumina scanning protocol

data_processing: Z score transformation for normalization was performed for each Illumina sample/array as previously described (Cheadle et al. J Mol Diagn, 5:73-81).

source_name: adrenal tumor

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 and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: ethnicity

value: Caucasian

value: child

value: primary pigmented nodular adrenocortical disease (PPNAD)

value: adrenal tumor


title: SC516_biopsy_gastric_tumor

description: Raw data file: T00279630.txt


title: SC535_biopsy_gastric_tumor

description: Raw data file: T00280632.txt


title: Gsa mutation 3

description: replicate 1

value: young adult

value: GNAS activating mutations


title: SC447_biopsy_gastric_tumor

description: Raw data file: T00279629.txt


title: Normal-36

description: Affymetrix


title: Mutant DPD25 time2 rep2

treatment_protocol: cultured in TSB medium supplemented with 25μM DPD to middle exponential phase


title: Cancer-4

description: Affymetrix


title: Gsa mutation 1

description: replicate 1


title: Cancer-LB14

description: Affymetrix


title: SC396_biopsy_gastric_tumor

description: Raw data file: T00276774.txt


title: PPNAD 2

description: replicate 1


title: SC505_biopsy_gastric_tumor

description: Raw data file: T00273636.txt


title: SC344_biopsy_gastric_tumor

description: Raw data file: T00276773.txt


title: SC485_biopsy_gastric_tumor

description: Raw data file: T00273634.txt


title: SC161_biopsy_gastric_tumor

description: Raw data file: T00276772.txt


title: PPNAD 1

description: replicate 1


title: Mutant DPD25 time1 rep1

treatment_protocol: cultured in TSB medium supplemented with 25μM DPD to early exponential phase


title: Mutant DPD25 time2 rep1


title: SC480_biopsy_gastric_tumor

description: Raw data file: T00273633.txt


title: Mutant DPD100 time4 rep1

treatment_protocol: cultured in TSB medium supplemented with 100μM DPD to stationary phase


title: Mutant DPD100 time4 rep2


title: Mutant DPD25 time1 rep2


title: Normal adrenal pool control 2

description: replicate 1

source_name: normal adrenal

value: pool (different ages)

value: normal adrenal


title: H295R 50uM 8Br-cAMP 24h replicate 3

city: Antwerp

first: Caroline

last: Vanparys

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

hyb_protocol: Agilent Gene Expression Hybridization protocol

scan_protocol: scanned using a Genetix Personal 4100A scanner; feature extration using the GenePix Pro analysis software 4.1

data_processing: VSN normalization

source_name: H295R Reference pool

label_protocol: Agilent Low RNA Input Amplification Kit (LRILAK) protocol

growth_protocol: H295R cells grown routinely in DMEM/F12 supplemented with 1% ITS-G and 2% UltroserSF serum; split 1/3

extract_protocol: Total RNA extracted using the Qiagen RNeasy mini kit

treatment_protocol: 8Br-cAMP dissolved in MilliQ water, blanks are solvent control samples, treatment in routine cell culture medium

tag: treatment

value: reference

source_name: H295R 50uM 8Br-cAMP 24h replicate 3

value: 50uM 8Br-cAMP

tag: time


title: Mutant DPD100 time3 rep2

treatment_protocol: cultured in TSB medium supplemented with 100μM DPD to late exponential phase

tag: strain


title: H295R 50uM 8Br-cAMP 24h replicate 2

source_name: H295R 50uM 8Br-cAMP 24h replicate 2


title: Normal adrenal pool control 1

description: replicate 1

value: normal


title: H295R 50uM 8Br-cAMP 24h replicate 1

source_name: H295R 50uM 8Br-cAMP 24h replicate 1


title: H295R 100uM 8Br-cAMP 24h replicate 3

source_name: H295R 100uM 8Br-cAMP 24h replicate 3

value: 100uM 8Br-cAMP


title: SC441_biopsy_gastric_tumor

description: Raw data file: T00270954.txt

value: gastric tissue

value: tumor


title: SC451_biopsy_gastric_tumor

description: Raw data file: T00270955.txt

value: F


title: MUC1 knockdown [siMUC1-C1] vs control

city: Porto

last: Costa

address: Rua Dr Roberto Frias s/n

country: Portugal

institute: IPATIMUP

hyb_protocol: Cy3- and Cy5-conjugated cDNA targets were then purified by QIAquick PCR purification columns, combined, vacuum-concentrated, and diluted to 55 µl with hybridization solution containing final concentrations of 50% formamide, 4.1x Denhardts, and 4.4x SSC.  To reduce nonspecific hybridization, the hybridization solution also contained final concentrations of 15 µg human Cot1 DNA (Invitrogen), 12µg poly-deoxyadenylate, and 5 µg of yeast tRNA (Sigma).  After clarification by centrifugation, the cDNA/hybridization solution was applied to DNA microarrays and incubated at 42ºC for 16-20 h.

scan_protocol: After hybridization, microarray slides were washed by immersion in 2X SSC, 0.1%SDS for 5 min at room temperature, 1X SSC, 0.01% SDS for 5 min at room temperature, and 0.2X SSC for 2 min at room temperature.  The microarrays were dried by centrifugation for 5 min at 1000 rpm and scanned immediately with a ScanArray 4000 confocal laser system (Perkin-Elmer).

data_processing:
Fluorescent intensities were background subtracted, and normalization and filtering of the data were performed using the QuantArray software package (Perkin-Elmer). Total background subtracted intensities for each channel were used for normalization. Differential expression was defined as those genes exhibiting a 2-fold up or down average ratio in signal intensity (after normalization).
The final processed data are ratios of Knockdown/controls (after normalization and background subtraction)

source_name: siMUC1-C1, gastric cancer cell line (MKN45)

label_protocol: To generate fluorescently-labeled single-stranded cDNA target, 40µg of total RNA was incubated with 2µg of anchored oligodeoxythymidylate primer in a total volume of 30µl at 70ºC for 10 min and chilled on ice.  To each sample was added 10X first strand buffer (6µl), 0.1M DTT (6µl), 20X aminoallyl-dNTP mix (3µl; 10mM dATP, 10mM dCTP, 10mM dGTP, 6mM dTTP, and 4mM aminoallyl-dUTP), RNase inhibitor (0.5µl) (RNasin, Promega), and StrataScript reverse transcriptase (3µl; 50U/µl).  After incubation at 48ºC for 60 min, an additional 50 units (1µl) of StrataScript was added to the samples and incubated for an additional 60 min. The reaction was stopped by adding 12 µl of 0.5M EDTA (pH 8).  Residual RNA was hydrolyzed by adding 12 µl of 1M NaOH to the mixture followed by incubation at 65ºC for 15 min and cooled to room temperature.  The reaction was neutralized with 16.8µl of 1N HCl.  First-strand cDNA was purified from unicorporated amino allyl-dUTPs on QIAquick PCR purification columns (Qiagen) according to manufacuter’s protocols, except that QIAquick wash buffer was replaced with 5 mM potassium phosphate buffer (pH 8.5) containing 80% ethanol, and cDNA was eluted with 4 mM potassium phosphate buffer (pH 8.5) and vacuum-dried.  cDNA was resuspended in 10 µl 0.05 M Na2CO3 buffer (pH 9), mixed with either Cy3 or Cy5 monofunctional NHS-ester (Amersham Pharmacia), and incubated for 90 min in the dark at room temperature.

extract_protocol: Total RNA was extracted from control and MUC1 RNAi MKN45 cells using the RNeasy kit with DNase I treatment.

value: medullary gastric cancer

value: MKN45 gastric carcinoma cells

tag: genotype/variation

value: MUC1 knockdown

source_name: SC, gastric cancer cell line (MKN45)

value: control


title: MUC1 knockdown [siMUC1-C2] vs control

source_name: siMUC1-C2, gastric cancer cell line (MKN45)


title: Gsa mutation 2

description: replicate 1

value: Caucasian


title: Mutant DPD100 time2 rep2

treatment_protocol: cultured in TSB medium supplemented with 100μM DPD to middle exponential phase

value: luxS negative


title: SC463_biopsy_gastric_tumor

description: Raw data file: T00270956.txt

source_name: gastric tissue, tumor


title: Mutant DPD100 time3 rep1


title: Normal adrenal pool control 3

description: replicate 1


title: SC421_biopsy_gastric_tumor

description: Raw data file: T00270953.txt

value: M


title: SNB-19 miR-182 Rep_1

city: Guangzhou

first: Jun

state: Guangdong

address: 74# Zhongshan Road II

department: Department of Biochemistry, Zhongshan School of Medicine

institute: Sun Yat Sen University

description: SNB-19 miR-182 transfection replicate 1, 36hr

hyb_protocol: Hybridization was performed in shanghai biochip corporation following standard Agilent protocol.

scan_protocol: Scanning was performed in shanghai biochip corporation following standard Agilent protocol.

data_processing: Data normalization and transformation was performed on Genespring GX 11 (Agilent) in shanghai biochip corporation.

source_name: SNB-19 miR-182 transfection replicate 1

label_protocol: Label was performed in shanghai biochip corporation following standard Agilent protocol.

growth_protocol: The glioma cells were cultured in complete DMEM medium and supplied with 10% FBS.

extract_protocol: Total RNA was isolated using RNeasy RNA isolation kit (Qiagen) following supplier’s protocol.

treatment_protocol: Transfection was performed following standard protocol of Lipofectamine 2000 transfection.

tag: transfection


title: H295R 100uM 8Br-cAMP 24h replicate 2

source_name: H295R 100uM 8Br-cAMP 24h replicate 2


title: H295R 300uM 8Br-cAMP 48h replicate 3

source_name: H295R 300uM 8Br-cAMP 48h replicate 3

value: 300uM 8Br-cAMP


title: H295R 100uM 8Br-cAMP 24h replicate 1

source_name: H295R 100uM 8Br-cAMP 24h replicate 1


title: Mutant DPD100 time1 rep2

treatment_protocol: cultured in TSB medium supplemented with 100μM DPD to early exponential phase


title: SNB-19 miRNA mimic negative control Rep_2

description: SNB19 miRNA mimic negative control transfection replicate 2, 36hr

value: miRNA mimic negative control


title: SNB-19 miR-182 Rep_2

description: SNB-19 miR-182 transfection replicate 2, 36hr

source_name: SNB-19 miR-182 transfection replicate 2


title: Mutant DPD100 time2 rep1

source_name: Mutant


title: H295R 300uM 8Br-cAMP 48h replicate 2

source_name: H295R 300uM 8Br-cAMP 48h replicate 2


title: Mutant DPD100 time1 rep1


title: H295R 300uM 8Br-cAMP 48h replicate 1

source_name: H295R 300uM 8Br-cAMP 48h replicate 1


title: H295R 300uM 8Br-cAMP 24h replicate 3

source_name: H295R 300uM 8Br-cAMP 24h replicate 3

source_name: H295R Reference pool


title: SNB-19 miRNA mimic negative control Rep_1

description: SNB19 miRNA mimic negative control transfection replicate 1, 36hr


title: control3

description:
biopsies of duodenum for experimental samples and full-thickness of duodenum (Clontech) for common reference
raw data file: CVID28.txt

hyb_protocol: Experimental and reference samples were co-hybridized using MAUI hybridization system as described by Schaupp et al. 2005; PMID: 15679093

data_processing: Signals were quantified using Agilent Feature Extraction Software Version 10.7.3.1. After subtraction of local background, signal intensity values were filtered to remove those lower than 10 and median (lowess) normalized using BRB Array Tools.

source_name: biopsy of duodenum

label_protocol: For human RNA, 50 ng was amplified and labeled using Aminoallyl RNA Amplification and Labeling System (NuGEN Technologies) following manufacturer’s protocol. Cy5-labeled samples were co-hybridized with a common reference RNA from normal duodenum (Clontech) labeled with Cy3 to Agilent Whole Human Genome Microarrays (GPL4133).

extract_protocol: tissues were homogenized in RLT buffer from Qiagen RNeasy KIT. Total RNA were isolated according to standard protocol

value: biopsy of duodenum

tag: disease status

value: control with unrelated pathologies

source_name: full-thickness of duodenum (Clontech)

value: full-thickness of duodenum (Clontech) reference

value: normal duodenum


title: patient3

description:
biopsies of duodenum for experimental samples and full-thickness of duodenum (Clontech)for common reference
raw data file: synt002.txt

growth_protocol: biopsies of duodenum for experimental samples and full-thickness of duodenum (Clontech) for common reference

value: CVID patient


title: Mutant time4 rep2

treatment_protocol: cultured in TSB medium to stationary phase


title: Mutant time4 rep1


title: Mutant time3 rep2

treatment_protocol: cultured in TSB medium to late exponential phase


title: Mutant time3 rep1


title: H295R 300uM 8Br-cAMP 24h replicate 2

source_name: H295R 300uM 8Br-cAMP 24h replicate 2

value: reference


title: Mutant time2 rep2

treatment_protocol: cultured in TSB medium to middle exponential phase


title: H295R 300uM 8Br-cAMP 24h replicate 1

source_name: H295R 300uM 8Br-cAMP 24h replicate 1


title: Mutant time2 rep1


title: Mutant time1 rep2

treatment_protocol: cultured in TSB medium to early exponential phase


title: H295R 300uM 8Br-cAMP 10h replicate 2

source_name: H295R 300uM 8Br-cAMP 10h replicate 2


title: H295R blank 48h replicate 2

source_name: H295R blank 48h replicate 2

value: blank


title: H295R blank 48h replicate 3

source_name: H295R blank 48h replicate 3


title: H295R 300uM 8Br-cAMP 10h replicate 1

source_name: H295R 300uM 8Br-cAMP 10h replicate 1


title: patient2

description:
biopsies of duodenum for experimental samples and full-thickness of duodenum (Clontech)for common reference
raw data file: CVID23.txt


title: patient1

description:
biopsies of duodenum for experimental samples and full-thickness of duodenum (Clontech)for common reference
raw data file: CVID22.txt


title: APP-1 time4 rep2

source_name: WT

value: serovar 1


title: Mutant time1 rep1


title: control1

description:
biopsies of duodenum for experimental samples and full-thickness of duodenum (Clontech)for common reference
raw data file: biopsy 3.txt


title: empty-vector expressor, biological rep 2

city: Hershey

first: David

last: Mu

state: PA

address: 500 University Dr H083

institute: Penn State Universitiy College of Medicine

hyb_protocol: Samples labeling/hybridization and data gathering were outsourced to Expression Analysis (Durham, NC) using the standard Affymetrix protocol.

data_processing: Expression values are calculated based on the difference of the PM signal and MM signal at each of the probe pairs using the Affymetrix GeneChip Operating System (GCOS). Log-transformed RMA normalization embedded with BRB Array Tool.

growth_protocol: NCI-H441 transfectant cells were cultured per ATCC guideline.

extract_protocol: Total RNAs were extracted with trizol.

treatment_protocol: Not applicable

value: empty vector


title: APP-1 time4 rep1


title: control2

description:
biopsies of duodenum for experimental samples and full-thickness of duodenum (Clontech)for common reference
raw data file: biopsy b.txt


title: APP-1 time3 rep2


title: mir-365-2 expressor, biological rep 2

scan_protocol: Samples labeling/hybridization and data gathering were outsourced to Expression Analysis (Durham, NC) using the standard Affymetrix protocol.


title: APP-1 time3 rep1


title: empty-vector expressor, biological rep 1

label_protocol: Samples labeling/hybridization and data gathering were outsourced to Expression Analysis (Durham, NC) using the standard Affymetrix protocol.


title: H295R blank 48h replicate 1

source_name: H295R blank 48h replicate 1


title: H295R blank 24h replicate 2

source_name: H295R blank 24h replicate 2


title: ES_FGFKO_NoGF_shRnd1_day3

city: Amsterdam

first: Bart A.

last: Westerman

address: De Boelelaan 1117

department: Cancer Center Amsterdam - Neurosurgery

country: Netherlands

institute: Cancer Center Amsterdam CCA

description: Growing FGF4 deficient ES cells infected a control shRNA knockdown vector (shRandom1, shRnd1) without FGF4 for three days prevents differentiation

hyb_protocol: Microarray analysis was performed using the MouseWG-6 v2 Expression BeadChip procedure of Illumina in Hybridization E1 Buffer

scan_protocol: Illumina's MouseWG-6 v2.0 Expression BeadChip offers the most up-to-date content for whole-genome expression profiling in the mouse. The multi-sample format lets researchers profile more than 45,200 transcripts and six samples simultaneously on a single BeadChip.

data_processing: CMFdb are processed with lumi(1) and VST transformed and RSN normalized using R script.

label_protocol: Samples were amplified using the Ambion Illumina® TotalPrep™ RNA Amplification Kit (Ambion AMIL1791) according to the manufacturer’s procedure.

growth_protocol: To measure the effect of FGF4 combined with Mp1 knockdown on transcriptional targets, FGF4 deficient ES cells were grown over night in serum free medium (N2B27) including Bmp4 at 10ng/ml.

extract_protocol: RNA was isolated using Trizol B (Invitrogen)

treatment_protocol: Cells were treated with FGF4 at a concentration of 20 ng/ml for 3 days (for samples 1-4, i.e. cells with Mp1 knockdown or shRnd controls), were treated with LIF at 10u/ml (Rnd1 controls, samples 5,6) or did not receive any growth factor at all (Rnd controls, samples 7,8)

value: FGF4-/- cells

value: R1 mESC line

value: 129X1/SvJ and 129S1/SV-+p+Tyr-cKitlSl-J/+ (Wilder et al, 1997)

tag: protocol


title: H295R blank 24h replicate 1

tag: cell line

source_name: H295R blank 24h replicate 1


title: ES_FGFKO_LIF_shRnd2_day3

description: Growing FGF4 deficient ES cells infected a control shRNA knockdown vector (shRandom2, shRnd2) in the presence of LIF for three days prevents differentiation


title: APP-1 time2 rep2


title: H295R blank 24h replicate 3

source_name: H295R blank 24h replicate 3


title: H295R blank 10h replicate 3

source_name: H295R blank 10h replicate 3


title: APP-1 time1 rep2


title: ES_FGFKO_LIF_shRnd1_day3

description: Growing FGF4 deficient ES cells infected a control shRNA knockdown vector (shRandom1, shRnd1) in the presence of LIF for three days prevents differentiation


title: APP-1 time2 rep1


title: H295R blank 10h replicate 1

source_name: H295R blank 10h replicate 1


title: H295R blank 10h replicate 2

source_name: H295R blank 10h replicate 2


title: mir-365-2 expressor, biological rep 1


title: ES_FGFKO_FGF_shRnd2_day3

description: Growing FGF4 deficient ES cells infected a control shRNA knockdown vector (shRandom2, shRnd2) for three days in the presence of FGF4 induces differentiation


title: APP-1 time1 rep1


title: SC495_biopsy_gastric_tumor

description: Raw data file: T00273635.txt

source_name: gastric tissue, tumor

tag: tissue

value: gastric tissue

value: tumor


title: ES_FGFKO_NoGF_shRnd2_day3

description: Growing FGF4 deficient ES cells infected a control shRNA knockdown vector (shRandom2, shRnd2) without FGF4 for three days prevents differentiation

tag: cell type


title: ES_FGFKO_FGF_shMP1G_day3

description: Growing FGF4 deficient ES cells infected with a Mp1 shRNA knockdown vector (using shMp1-G) for three days in the presence of FGF4 prevents differentiation


title: ES_FGFKO_FGF_shRnd1_day3

description: Growing FGF4 deficient ES cells infected a control shRNA knockdown vector (shRandom1, shRnd1) for three days in the presence of FGF4 induces differentiation


title: Rat liver LE Corn Oil 4 days rep3

status: Public on Nov 14 2011

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

data_processing: Quantitated array data (CEL files) were loaded into the R statistical environment (v2.7.2) using the Affy package (v1.18.2) of the BioConductor library. Data was investigated for spatial and distributional homogeneity, then pre-processed with a sequence-specific version of the RMA algorithm termed GCRMA, as implemented in R (v2.12.1). We employed an updated and remapped mapping of Probes to Entrez Gene IDs as implemented in the R package rat2302rnentrezgcdf (v11.0.0).

organism: Rattus norvegicus

source_name: liver, Long-Evans, Corn Oil treated, 4 day exposure

growth_protocol: Animals were grown in a 12h/12h light/dark cycle housed in groups of 4 rats in suspended stainless-steel wire-mesh cages with pelleted R36 feed and tap water. The temperature was 21 +/- 1 degree Celcius and the relative humidity 50% +/- 10%.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: TCDD treated animals were treated with 100 ug/kg TCDD by oral gavage.

tag: Gender

value: Male,Tissue:liver,Strain:Long-Evans,Age:10-12 weeks,Treatment:Corn Oil vehicleFeed:ad libitum,Exposure:4 days


title: Rat liver LE Feed Restricted 10 days rep1

scan_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

source_name: liver, Long-Evans, Corn Oil treated, Feed-Restricted, 10 day exposure

value: Male,Tissue:liver,Strain:Long-Evans,Age:10-12 weeks,Treatment:Corn Oil vehicleFeed:restricted,Exposure:10 days


title: Rat liver HW TCDD 10 days rep3

data_processing: Quantitated array data (CEL files) were loaded into the R statistical environment (v2.9.2) using the Affy package (v1.22.1) of the BioConductor library. Data was investigated for spatial and distributional homogeneity, then pre-processed with a sequence-specific version of the RMA algorithm termed GCRMA, as implemented in R (v2.16.0). We employed an updated and remapped mapping of Probes to Entrez Gene IDs as implemented in the R package rat2302rnentrezgcdf (v12.0.0).

source_name: liver, Han/Wistar, TCDD treated, 10 day exposure

label_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

tag: gender

value: Male,Tissue:liver,Strain:Han/WistarAge:10-12 weeks,Treatment:100 ug/kg TCDD,Feed:ad libitum,Exposure:10 days


title: Rat liver LE TCDD 10 days rep4

source_name: liver, Long-Evans, TCDD treated, 10 day exposure

value: Male,Tissue:liver,Strain:Long-Evans,Age:10-12 weeks,Treatment:100 ug/kg TCDD,Feed:ad libitum,Exposure:10 days


title: Rat liver LE Corn Oil 4 days rep4


title: Rat liver LE Corn Oil 10 days rep3

source_name: liver, Long-Evans, Corn Oil treated, 10 day exposure

value: Male,Tissue:liver,Strain:Long-Evans,Age:10-12 weeks,Treatment:Corn Oil vehicleFeed:ad libitum,Exposure:10 days


title: Rat liver LE TCDD 10 days rep2


title: Rat liver HW Corn Oil 10 days rep5

source_name: liver, Han/Wistar, Corn Oil treated, 10 day exposure

value: Male,Tissue:liver,Strain:Han/WistarAge:10-12 weeks,Treatment:Corn Oil vehicle,Feed:ad libitum,Exposure:10 days


title: Rat liver HW Corn Oil 10 days rep2


title: Rat liver HW Corn Oil 10 days rep1


title: Rat liver LE Corn Oil 10 days rep5


title: Rat liver LE TCDD 10 days rep3


title: Rat liver HW TCDD 10 days rep4


title: Rat liver HW Corn Oil 10 days rep3


title: Rat liver LE Feed Restricted 10 days rep2


title: Rat liver LE Corn Oil 10 days rep2


title: Rat liver LE Corn Oil 10 days rep4


title: Rat liver HW TCDD 10 days rep5


title: Rat liver HW TCDD 10 days rep1


title: Rat liver LE Corn Oil 10 days rep1


title: Rat liver LE Feed Restricted 4 days rep4

source_name: liver, Long-Evans, Corn Oil treated, Feed-Restricted, 4 day exposure

value: Male,Tissue:liver,Strain:Long-Evans,Age:10-12 weeks,Treatment:Corn Oil vehicleFeed:restricted,Exposure:4 days


title: Rat liver LE Feed Restricted 4 days rep3


title: Rat liver LE Feed Restricted 10 days rep3


title: Rat liver LE TCDD 10 days rep5


title: Rat liver HW TCDD 10 days rep2


title: ES_FGFKO_FGF_shMp1Lib_day3

description: Growing FGF4 deficient ES cells infected with a Mp1 shRNA knockdown vector (using shMp1-Lib) for three days in the presence of FGF4 prevents differentiation


title: Rat liver LE TCDD 10 days rep1


title: Rat liver HW Corn Oil 10 days rep4


title: Rat liver HW Corn Oil 4 days rep4

source_name: liver, Han/Wistar, Corn Oil treated, 4 day exposure

value: Male,Tissue:liver,Strain:Han/WistarAge:10-12 weeks,Treatment:Corn Oil vehicleFeed:ad libitum,Exposure:4 days


title: Rat liver HW Corn Oil 4 days rep3


title: Rat liver LE Feed Restricted 4 days rep2


title: Rat liver HW TCDD 4 days rep3

source_name: liver, Han/Wistar, TCDD treated, 4 day exposure

value: Male,Tissue:liver,Strain:Han/WistarAge:10-12 weeks,Treatment:100 ug/kg TCDD,Feed:ad libitum,Exposure:4 days


title: Rat liver LE Feed Restricted 10 days rep4


title: Rat liver HW Corn Oil 4 days rep2


title: Rat liver LE Feed Restricted 10 days rep5


title: Rat liver LE TCDD 4 days rep1

source_name: liver, Long-Evans, TCDD treated, 4 day exposure

value: Male,Tissue:liver,Strain:Long-Evans,Age:10-12 weeks,Treatment:100 ug/kg TCDD,Feed:ad libitum,Exposure:4 days


title: Rat liver LE Corn Oil 4 days rep1


title: Rat liver LE TCDD 4 days rep4


title: Rat liver LE TCDD 4 days rep3


title: Rat liver HW TCDD 4 days rep1


title: Rat liver LE TCDD 4 days rep2


title: Rat liver LE Corn Oil 4 days rep2


title: Rat liver LE Feed Restricted 4 days rep1


title: Rat liver HW Corn Oil 4 days rep1


title: Rat liver HW TCDD 4 days rep4


title: Rpl11_polysomal sample_bilogical replicate 1

city: Rotterdam

first: Erdogan

last: Taskesen

address: dr. molewaterplein 50

institute: Erasmus University Medical Center (EMC)

hyb_protocol: Affymetrix protocol.

scan_protocol: Affymetrix protocol.

data_processing: Affymetrix Microarray Suite 5 (MAS5) with global scaling to target value 100. Probe sets with polyribosomal intensity lower than 100 were excluded. Subsequently, the intensity values were normalized per probe set for each sample within the associated class to quantify the mRNA transcript association with polyribosomes. These are computed by taking the polyribosomal intensity value per probe set of each sample with respect to the total intensity value within the sample. This resulted into translational ratios that range between 0 and 1.

source_name: erythrobalsts

label_protocol: Affymetrix protocol.

growth_protocol: Immortalized erythroblasts were expanded under the Epo/SCF/Dex in serum free media.

extract_protocol: 7 ug of RNA was extracted from collected fractions from sucrose gradients profile such, that polyribosomes up to 80S peak were pooled and designated poly sample and the rest of the fractions were pooled and designated sub fractions.

treatment_protocol: 3 days after shRNA lentiviral delivery the cells were treated with cycloheximide, harvested and frozen on nitrogen.

tag: shRNA

tag: fraction

value: poly


title: Rpl11_subpolysomal sample_bilogical replicate 2

value: sub


title: Rat liver HW TCDD 4 days rep2


title: BT16 cells, treated with IC25 of SNDX275

city: Aurora

first: Diane

middle: K

last: Birks

state: CO

department: Neurosurgery

institute: University of Colorado, Denver - Anschutz Medical Campus

description: Atypical Teratoid / Rhabdoid Tumor cell line

hyb_protocol: For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to  the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).

scan_protocol: All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).

data_processing: Data were background corrected and normalized using the gcRMA algorithm, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.

molecule: polyA RNA

label_protocol: Five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer.  For sample ID03161, limited amount of starting RNA precluded use of this protocol. Instead ID03161 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.

growth_protocol: Cells were grown in RPMI-1640 supplemented with 10% FBS at 37C with 5% CO2

extract_protocol: RNA was extracted from each sample using an RNeasy kit (Qiagen) according to the manufacturer’s directions

treatment_protocol: Cells were plated and subsequently treated for 24hr with IC25 concentrations of SNDX-275 (Sigma), or equivalent doses of DMSO (control).

value: atypical teratoid/rhabdoid tumor cells


title: eIF2B R132H/R132H mutant brain at P21, biological rep3

city: Tel Aviv

first: Liraz

last: Marom

address: Department of Cell Research and Immunology Tel Aviv University

department: Cell Research and Immunology

country: Israel

institute: Tel Aviv University

description:
eIF2Bmut P21_c
Gene expression data from brain at postnatal day 21

scan_protocol: according to the instruction manual, as described in the Affymetrix website.

data_processing: Microarray data were normalized using RMA

source_name: eIF2B R132H/R132H mutant brain at P21

label_protocol: 300ng total RNA underwent first-strand and second strand cDNA synthesis. Complementary RNA was generated and used to produce sense-strand cDNA, which was fragmented and end-labeled with biotin. Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

extract_protocol: Total RNA from brain tissues (without the cerebellum) was isolated using Trizol reagent according to the manufacturer's protocol (Invitrogen). RNA samples for microarray analysis were further cleaned using Phase Lock Gel (Eppendorf). RNA quality was assessed by its absorbance at 260nm and 280nm using a NanoDrop spectrophotometer and its integrity was assessed by agarose gel electrophoresis.

value: brain, not incuding cerebellum

value: eIF2B-R132H/R132H mutant

tag: developmental stage

value: postnatal day21


title: Rps19_polysomal sample_bilogical replicate 3


title: Rpl11_polysomal sample_bilogical replicate 2


title: Rpl11_subpolysomal sample_bilogical replicate 1


title: BT16 cells, not treated (DMSO only)

source_name: BT16 cells, not treated (DMSO only)


title: BT12 cells, treated with IC25 of SNDX275


title: Rpl11_polysomal sample_bilogical replicate 3


title: Rpl11_subpolysomal sample_bilogical replicate 3


title: eIF2B R132H/R132H mutant brain at P21, biological rep2

description:
eIF2Bmut P21_b
Gene expression data from brain at postnatal day 21

hyb_protocol: according to the instruction manual, as described in the Affymetrix website


title: Rps19_subpolysomal sample_bilogical replicate 3


title: Rps19_subpolysomal sample_bilogical replicate 2


title: eIF2B R132H/R132H mutant brain at P21, biological rep1

description:
eIF2Bmut P21_a
Gene expression data from brain at postnatal day 21


title: Environmental sample D10_11 (Myk7)

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

institute: University of Bayreuth

description:
Myk7
Two independent samples (11 and 12) taken at the same sampling site

hyb_protocol: 1 µl of a 1:125 dilution of labelled RNA were combined with Agilent's blocking agent and hybridization buffer (total 50 µl) and hybridized to one subarray Labelled RNA samples (1 µl) were added directly and in a fivefold dilution to the Agilent's Gene Expression Hybridisation Solution; hybridisation was carried out at 65°C for 18 hours in an Agilent's hybridisation oven; microarrays were washed with Agilent's Wash Buffer Kit; Ozone-mediated Cy5 degradation was inhibited by applying Agilent's Stabilisation and Drying Solution.

scan_protocol: Microarrays were scanned using a FLA8000 scanner (Fuji) at 5 µm resolution and confocal signal capturing mode

data_processing:
Spot intensities were quantified using ArrayVision software (GE Healthcare) and values were calculated as background-corrected, artefact-removed volume per spot; spot segmentation was allowed to correct for different spot morphologies. Cy5 values were normalized to Cy3 values using the signal ratio (Cy3/Cy5) of  Eukarya SSU rRNA probe signals present in four replicates on each subarray (Note: Cy3 values remained unchanged; they are identical to the background corrected raw values).
Probes such as internal controls were filtered out and will not appear in the associated publication. In the publication only the 11.3 k probes will be discussed and, therefore, only these probes are presented in the data table.

organism: soil metagenome

source_name: Environmental sample (pine forest soil)

label_protocol: 1.5 µg total RNA was labelled using the CyScribe Drect mRNA Labelling Kit (GE Healthcare); total volume was 11 µl.

growth_protocol: Samples were harvested from pine forest soil near Bayreuth, Germany (49°58'16'' N, 11°34'51'' E and 460 m alt.)

extract_protocol: Samples were extracted as described in Peršoh et al. (2008), J. Microbiol. Meth. 75:19-24

tag: sample type

value: pine forest soil microorganisms

tag: geographical location

tag: rna sample dilution used in hybn

value: 1:125 dilution of labelled RNA


title: eIF2B R132H/R132H mutant brain at P18, biological rep1

description:
eIF2Bmut P18_a
Gene expression data from brain at postnatal day 18

source_name: eIF2B R132H/R132H mutant brain at P18

value: postnatal day18


title: eIF2B R132H/R132H mutant brain at P18, biological rep2

description:
eIF2Bmut P18_b
Gene expression data from brain at postnatal day 18


title: BT12 cells, not treated (DMSO only)

source_name: BT12 cells, not treated (DMSO only)


title: wild-type brain at P21, biological rep2

description:
WT P21_b
Gene expression data from brain at postnatal day 21

source_name: wild-type brain at P21

value: wild-type


title: Rps19_subpolysomal sample_bilogical replicate 1


title: wild-type brain at P21, biological rep3

description:
WT P21_c
Gene expression data from brain at postnatal day 21


title: Environmental sample D10_12 (Myk8)

description:
Myk8
Two independent samples (11 and 12) taken at the same sampling site

value: near Bayreuth, Germany (49°58'16'' N, 11°34'51'' E and 460 m alt.)


title: wild-type brain at P21, biological rep1

description:
WT P21_a
Gene expression data from brain at postnatal day 21


title: Rps19_polysomal sample_bilogical replicate 1


title: Environmental sample D10_12 (Myk6)

description:
Myk6
Two independent samples (11 and 12) taken at the same sampling site

hyb_protocol: 1 µl of a 1:25 dilution of labelled RNA were combined with Agilent's blocking agent and hybridization buffer (total 50 µl) and hybridized to one subarray Labelled RNA samples (1 µl) were added directly and in a fivefold dilution to the Agilent's Gene Expression Hybridisation Solution; hybridisation was carried out at 65°C for 18 hours in an Agilent's hybridisation oven; microarrays were washed with Agilent's Wash Buffer Kit; Ozone-mediated Cy5 degradation was inhibited by applying Agilent's Stabilisation and Drying Solution.

value: 1:25 dilution of labelled RNA


title: wild-type brain at P18, biological rep1

description:
WT P18_a
Gene expression data from brain at postnatal day 18

source_name: wild-type brain at P18


title: eIF2B R132H/R132H mutant brain at P1, biological rep2

description:
eIF2Bmut P1_b
Gene expression data from brain at postnatal day 1

source_name: eIF2B R132H/R132H mutant brain at P1

value: postnatal day1


title: Environmental sample D10_11 (Myk5)

description:
Myk5
Two independent samples (11 and 12) taken at the same sampling site


title: ev_subpolysomal sample_bilogical replicate 3

value: sc


title: eIF2B R132H/R132H mutant brain at P1, biological rep3

description:
eIF2Bmut P1_c
Gene expression data from brain at postnatal day 1


title: wild-type brain at P18, biological rep3

description:
WT P18_c
Gene expression data from brain at postnatal day 18


title: ev_polysomal sample_bilogical replicate 3


title: Environmental sample D10_12 (Myk2)

description:
Myk2
Two independent samples (11 and 12) taken at the same sampling site

hyb_protocol: 1 µl of labelled RNA were combined with Agilent's blocking agent and hybridization buffer (total 50 µl) and hybridized to one subarray Labelled RNA samples (1 µl) were added directly and in a fivefold dilution to the Agilent's Gene Expression Hybridisation Solution; hybridisation was carried out at 65°C for 18 hours in an Agilent's hybridisation oven; microarrays were washed with Agilent's Wash Buffer Kit; Ozone-mediated Cy5 degradation was inhibited by applying Agilent's Stabilisation and Drying Solution.

value: undiluted labelled RNA


title: ev_subpolysomal sample_bilogical replicate 2


title: ev_polysomal sample_bilogical replicate 2


title: wild-type brain at P18, biological rep2

description:
WT P18_b
Gene expression data from brain at postnatal day 18


title: wild-type brain at P1, biological rep3

description:
WT P1_c
Gene expression data from brain at postnatal day 1

source_name: wild-type brain at P1


title: Environmental sample D10_11 (Myk3)

description:
Myk3
Two independent samples (11 and 12) taken at the same sampling site

hyb_protocol: 1 µl of a 1:5 dilution of labelled RNA were combined with Agilent's blocking agent and hybridization buffer (total 50 µl) and hybridized to one subarray Labelled RNA samples (1 µl) were added directly and in a fivefold dilution to the Agilent's Gene Expression Hybridisation Solution; hybridisation was carried out at 65°C for 18 hours in an Agilent's hybridisation oven; microarrays were washed with Agilent's Wash Buffer Kit; Ozone-mediated Cy5 degradation was inhibited by applying Agilent's Stabilisation and Drying Solution.

value: 1:5 dilution of labelled RNA


title: wild-type brain at P1, biological rep1

description:
WT P1_a
Gene expression data from brain at postnatal day 1


title: wild-type brain at P1, biological rep2

description:
WT P1_b
Gene expression data from brain at postnatal day 1


title: Environmental sample D10_12 (Myk4)

description:
Myk4
Two independent samples (11 and 12) taken at the same sampling site


title: eIF2B R132H/R132H mutant brain at P1, biological rep1

description:
eIF2Bmut P1_a
Gene expression data from brain at postnatal day 1


title: Environmental sample D10_11 (Myk1)

description:
Myk1
Two independent samples (11 and 12) taken at the same sampling site


title: ev_polysomal sample_bilogical replicate 1


title: ev_subpolysomal sample_bilogical replicate 1


title: Endometrial biopsy_ETB67_CD146-/PDGFRB+

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: GeneSpringGX 8.0, Microarray Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1, Summarization Algorithm: ExonRMA16, Normalization: Quantile, Baseline Transformation: median of all samples

source_name: Endometrial biopsy_ETB67

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN FFPE kit, and sense-strand cDNA targets were created using the NuGEN WT-Ovation Exon Module, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

extract_protocol: FACS analyzed sorted cell populations were subject to RNA isolation and purification, with DNAse treatment, using Pico Pure RNA Isolation Kit

tag: age (years)

value: endometrium

tag: phase

value: Early Secretory

tag: cycle day

tag: cd146 and pdgfrb expression


title: Endometrial biopsy_ETB67_CD146+/PDGFRB-


title: Paired adjacent non-cancer tissue Replicate 2

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

description: Biological replicate 2 of 3,adjacent non-cancer tissue,colorectal cancer patient

hyb_protocol: According to the instructions of Agilent Oligo aCGH  Hybridization Kit

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent GeneSpring GX 11.5 was used for background subtraction and LOWESS normalization. Following global mean normalization, probes with an intensity <300 were discarded from further analysis.

source_name: methylated CpG-island recovery assay (MIRA) enriched,adjacent non-cancer tissue,colorectal cancer patient 2

label_protocol: The products of whole genome amplification from the total input DNA without MBD enrichment and from methylation-enriched DNA were purified by using DNA purification kit, respectively. The purified DNA fragments were then labeled with cy3-dCTP or cy5-dCTP with Klenow enzyme (Takara) according to the instruction of the manufacturer.

extract_protocol: DNA was isolated from fresh frozen tissues using standard phenol/chloroform method.

value: adjacent non-cancer

tag: patient

value: methylated DNA-enriched

source_name: Input, adjacent non-cancer tissue,colorectal cancer patient 2

value: Input


title: Endometrial biopsy_ETB74_CD146+/PDGFRB+

source_name: Endometrial biopsy_ETB74


title: Endometrial biopsy_ETB74_CD146-/PDGFRB+


title: wt_subpolysomal sample_biological replicate 2

value: sub


title: Endometrial biopsy_ETB65_CD146+/PDGFRB+

source_name: Endometrial biopsy_ETB65

value: Proliferative


title: Endometrial biopsy_ETB65_CD146+/PDGFRB-


title: wt_subpolysomal sample_biological replicate 3


title: Paired adjacent non-cancer tissue Replicate 3

description: Biological replicate 3 of 3,adjacent non-cancer tissue,colorectal cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,adjacent non-cancer tissue,colorectal cancer patient 3

source_name: Input, adjacent non-cancer tissue,colorectal cancer patient 3


title: Endometrial biopsy_ETB74_CD146+/PDGFRB-


title: Endometrial biopsy_ETB67_CD146+/PDGFRB+


title: Endometrial biopsy_ETB65_CD146-/PDGFRB+


title: wt_polysomal sample_biological replicate 3

source_name: erythrobalsts

value: poly


title: Colorectal cancer tissue Replicate 2

description: Biological replicate 2 of 3,cancer tissue,colorectal cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,cancer tissue,colorectal cancer patient 2

value: colorectal cancer

source_name: Input, cancer tissue,colorectal cancer patient 2


title: wt_polysomal sample_biological replicate 2


title: Endometrial biopsy_ETB61_CD146+/PDGFRB+

source_name: Endometrial biopsy_ETB61

value: Interval


title: wt_polysomal sample_biological replicate 1


title: Paired adjacent non-cancer tissue Replicate 1

description: Biological replicate 1 of 3,adjacent non-cancer tissue,colorectal cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,adjacent non-cancer tissue,colorectal cancer patient 1

source_name: Input, adjacent non-cancer tissue,colorectal cancer patient 1


title: Endometrial biopsy_ETB61_CD146-/PDGFRB+


title: wt_subpolysomal sample_biological replicate 1


title: Endometrial biopsy_ETB61_CD146+/PDGFRB-