title: Met 3 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359479

value: pulmonary metastasis of clear-cell renal cell carcinoma (laser resection)

value: DFS = 95 months


title: Chronic Lymphocytic Leukemia (CLL) sample 6 Jel025U133A

status: Public on Jun 25 2010

type: RNA

city: Rochester

first: Brian

last: Bot

state: MN

address: 200 1st Street SW

country: USA

institute: Mayo Clinic

description: Gene expression data from peripheral blood B cells from patients diagnosed with CLL prior to treatment

hyb_protocol: 15ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human U133 A and B GeneChips® . GeneChips were washed and stained following the Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA

scan_protocol: Hybridized arrays were scanned using a GeneChip® 3000 scanner

data_processing: Affymetrix GeneChip® Operating System software v.1.3 (Santa Clara, CA) were used to quantitatively analyze the scanned image

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Purified CLL B cells from peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Enzo, New York, NY).

extract_protocol: Total RNA isolation by the Trizol method following manufacturer's protocol from purified B cells

tag: disease state

value: CLL

tag: cell type


title: Chronic Lymphocytic Leukemia (CLL) sample 8 Jel027U133A

value: Purified CLL B cells from peripheral blood


title: dme-miR-310 cluster  knockout, biological rep3

city: Guangzhou

first: TIAN

last: TANG

address: Xingangxi Rd. #135

country: China

institute: Sun Yat-Sen University

description: Expression data from the third-instar larvae of miR310 cluster knockout stock

hyb_protocol: standard hybridization protocol as described in GeneChip® Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G. Images were quantified using GeneChip Operating Software Version 1.4 (GCOS)

data_processing: Data was quantile normalized using CisGenome

label: biotin

organism: Drosophila melanogaster

source_name: larvae of miR310 cluster knockout stock with the imprecise P-element excision of the P{EP}2587 insertion

label_protocol: Invitrogen Bioprime random labeling

growth_protocol: All stocks were maintained on yeast-cornmeal agar at 25C on a 12h L/D cycle.

extract_protocol: Total RNA was extracted using Trizol followed by the purification with RNeasy Mini kit (QIAGEN)

treatment_protocol: We collected 3rd instar progeny larvae from the stocks with precise and imprecise excision of the P{EP}2587 insertion.

tag: developmental stage

value: third-instar larvae


title: Chronic Lymphocytic Leukemia (CLL) sample 2 Jel019U133A


title: Met 6 reanalysis

city: Dresden

first: Wuttig

last: Daniela

address: Fetscherstr. 74

department: Department of Urology

country: Germany

institute: Dresden, University of Technology

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359482

hyb_protocol: Following fragmentation, 20 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip HGU133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS3000 7G Scanner (Affymetrix).

data_processing:
data for analysis:
study I: Met1-9, Met11-18, Met20, Met23, Met25 (n=20); study II: all samples (n=48)
Global background correction, quantile normalization and signal calculation were carried out using the RMAExpress 4.1 software. Data of primary ccRCC were batch corrected using the combat modul after all probe sets with less than 5/48 present signals were excluded. Data of all samples were filtered (max-min > 100; max/min > 3; ceiling = 16000, threshold = 20).

source_name: pulmonary metastasis of clear-cell renal cell carcinoma (laser resection)

label_protocol: Biotinylated cRNA were prepared according to the One-Cycle Target Labeling and Control Reagents Kit protocol (Affymetrix, Santa Clara, USA) from 1.0 - 2.5 µg total RNA.

extract_protocol:
Metastases were obtained during precise laser-based resection (1318 nm neodynium-YAG, Coswig Specialized Hospital). Primary ccRCC were obtained by (partial) nephrectomy in the Departments of Urology in the University Hopitals Dresden or Jena.
Cryo-sections (4 um) of snap-frozen tissue samples were made and homogenized using QiaShredder (Qiagen, Hilden, Germany)
RNA was isolated with the RNeasy Mini Kit (Qiagen) with additional DNA digestion (RNase-Free DNase Set, Qiagen).

tag: gender

value: male

tag: tissue

tag: dfs/follow-up

value: DFS = 38 months

tag: no. of pulmonary metastases

tag: date of sample preparation and hybridisation


title: Met 9 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359485

value: DFS = 9 months


title: Normal B Cell Control 2 Jel024U133A-restain

description: Gene expression data from peripheral blood  B cells age matched normal controls

source_name: Purified B cells from peripheral blood from donors 60 years of age and older

value: normal


title: Chronic Lymphocytic Leukemia (CLL) sample 4 Jel022U133A


title: Chronic Lymphocytic Leukemia (CLL) sample 3 Jel021U133A


title: Met 1 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359477

value: DFS = 1 month


title: Met 11 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359486

value: DFS = 31 months


title: Met 2 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359478

value: DFS = 15 months


title: Met 7 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359483

value: DFS = 10 months


title: Met 4 reanalysis

description:
in case of metastases, the DFS is the time from nephrectomy to the diagnosis of the metastases; follow-up is shown for patients who did not develop macroscopic metastases
reanalysis of GSE14378 Sample GSM359480

value: female

value: DFS = 12 months


title: Chronic Lymphocytic Leukemia (CLL) sample 7 Jel026U133A


title: Chronic Lymphocytic Leukemia (CLL) sample 1 Jel018U133A


title: dme-miR-310 cluster  knockout, biological rep2


title: Normal B Cell Control 1 Jel020U133A

value: Purified B cells from peripheral blood from donors 60 years of age and older


title: dme-miR-310 cluster  knockout, biological rep1


title: CardiacMuscle_80mg/kgRosi_336hrs_rep3

city: Watertown

first: Mary

last: Simcox

state: MA

address: 500 Arsenal St

institute: Forma Therapeutics

hyb_protocol: Standard Affymetrix Protocols

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: GCOS software using MAS5

organism: Rattus norvegicus

source_name: Cardiac muscle sampled 336 hrs post 80 mg/kgrosiglitazone once daily for 14 days

label_protocol: Affymetrix One-Cycle Target Labeling Assay using Affymetrix kit P/N 900493

extract_protocol: Qiagen RNAeasy minikit with Dnase treatment according to manufacturers recommendations

treatment_protocol: Cardiac muscle was isolated from the rat, cut sagitally, scored and placed quickly into RNAlater.  After 24 hours at 4C, tissues were moved to -80C for storage until all tissues were harvested.

tag: strain

value: Wistar


title: CardiacMuscle_80mg/kgRosi_168hrs_rep6

source_name: Cardiac muscle sampled 168 hrs post 80 mg/kgrosiglitazone once daily for 14 days


title: CardiacMuscle_80mg/kgRosi_336hrs_rep4


title: CardiacMuscle_80mg/kgRosi_336hrs_rep5


title: CardiacMuscle_80mg/kgRosi_336hrs_rep2


title: CardiacMuscle_80mg/kgRosi_168hrs_rep4


title: CardiacMuscle_80mg/kgRosi_336hrs_rep1


title: spermatozoa from asthenozoospermic men

city: Shenzhen

first: Jing

last: Chen

state: Guangdong

address: NO.1120 Lianhua Rd

department: Laboratory of Male Reproductive Medicine and Genetics

institute: Peking University Shenzhen Hospital

description: Gene expression data from spermatozoa of asthenozoospermic men

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Human GenomeU133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: pooled ejaculated spermatozoa from 30 asthenozoospermic men

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA .

extract_protocol:
Semen was collected by masturbation after 3 days of sexual abstinence and allowed to liquefy for 30–60 min at room temperature. A semen analysis was performed by computer-assisted sperm analysis (CASA) system according to WHO (Word Health Organization 1999) guidelines.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Liquefied semen samples were fractionated by Percoll on a discontinuous density gradients consisting of four successive layers with the following densities: four layers: 47.5%, 57%, 76% and 95%. The spermatozoa were collected from the interface 57%-76% and the under layer of 95%, then washed three times with PBS. 30 purified spermatozoa of each group were pooled before being used.

value: ejaculated spermatozoa

tag: genotype

value: chinese with black eyes, black hair and yellow skin

tag: age

value: men aged 20 to 40 years


title: CardiacMuscle_80mg/kgRosi_168hrs_rep5


title: dme-miR-310 cluster  knockout control, biological rep3

description: Expression data from the third-instar larvae of miR310 cluster knockout control

source_name: larvae of miR310 cluster knockout control stock with the precise P-element excision of the P{EP}2587 insertion


title: spermatozoa from normozoospermic men

description: Gene expression data from spermatozoa of normozoospermic men

source_name: pooled ejaculated spermatozoa from 30 normozoospermic men


title: dme-miR-310 cluster  knockout control, biological rep2


title: 01UNN

city: Cincinnati

first: Michael

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard scanning

data_processing: Data were imported into GeneSpring 7.3 with RMA preprocessing and normalized to median of all samples.  Normalized data were exported and subjected to Distance Weighted Discrimination (DWD) to account for any batch effects then reimported into Gene Spring and analyzed.

source_name: Psoriatic

label_protocol: NuGEN Ovation labeling

extract_protocol: Peripheral blood was drawn and PBMC were isolated over Ficoll.  Samples were stored in Trizol at -80oC until extracted according to manufacturers directions.

tag: original diagnosis

value: Psoriatic

value: Peripheral blood mononuclear cells


title: 01UN0


title: Chronic Lymphocytic Leukemia (CLL) sample 21 Jel047A

value: CLL

value: Purified CLL B cells from peripheral blood


title: dme-miR-310 cluster  knockout control,biological rep1

value: third-instar larvae


title: control line w1118,biological rep3

description: Expression data of Gal4/w1118 larvae

source_name: progeny from the cross with maternal GAL4 line NP5941 and paternal w1118

treatment_protocol: We collected 3rd instar progeny larvae from the crosses with maternal NP5941 and paternal UAS-miR-310 cluster transgenic lines and used 3rd instar larvae from the cross with maternal NP5941 and paternal w1118 as control.

tag: development stage


title: control line w1118,biological rep2

description: Expression data of Gal4/w1118 larvae


title: control line w1118,biological rep1

description: Expression data of Gal4/w1118 larvae


title: Dp310s line P4-18,biological rep3

description: Expression data of Gal4/UAS-Dp310s larvae

source_name: progeny from the cross with maternal GAL4 line NP5941 and paternal UAS-dp310s line P4-18


title: 01N1R

source_name: PolyRF+

value: PolyRF+


title: 01LPM

source_name: ExtendedOligo

value: ExtendedOligo


title: CardiacMuscle_80mg/kgRosi_168hrs_rep3

value: male


title: CardiacMuscle_80mg/kgRosi_168hrs_rep2


title: CardiacMuscle_80mg/kgRosi_24hrs_rep6

source_name: Cardiac muscle sampled 24 hrs post 80 mg/kgrosiglitazone once daily for 14 days


title: CardiacMuscle_80mg/kgRosi_168hrs_rep1


title: 01LMR

source_name: PolyRF-

value: PolyRF-


title: CardiacMuscle_80mg/kgRosi_24hrs_rep3


title: Dp310s line P4-18,biological rep2


title: 01MHB


title: WT embryonic stem cells (ESCs, J1), H3K27me3 ChIP-chip (1/2), exp1

type: genomic

city: Los Angeles

first: Yi

last: Sun

state: CA

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

hyb_protocol: 5 ug Cy3- or Cy5-labelled DNA were combined and hybridized to the Agilent 244K mouse extended promoter microarray (G4490A, 2-array set, genomic build: mm7) for 40 h at 65 ˚C (10 r.p.m.). Microarrays were washed according to Agilent's standard procedures.

scan_protocol: Microarry slides were scanned on at 5-micron resolution using an Agilent Technologies Scanner G2505B (US23502366).

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_ESC_H3K27me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

molecule: genomic DNA

organism: Mus musculus

source_name: WT ESC, whole cell extract

label_protocol: Whole cell extract and immunoprecipitated DNA were amplified using the Whole Genome Amplification Kit (Sigma), and 2 ug of amplified products was labeled with Cy3- and Cy5-dUTP (Perkin Elmer) using Bioprime DNA labeling system (Invitrogen).

growth_protocol: Postnatal day 14-21 day mouse lateral ventricle walls were dissected and mechanically dissociated. Single cell suspensions were plated at low density (10,000~20,000 cells cm-2) on cell culture dishes coated with poly-L-ornithine (PO)/fibronectin (FN), allowing individual cells to form spatially distinct colonies. Serial passage (less than 2 passages, or 2 weeks) allowed us to enrich undifferentiated NSCs to high purity (>95% Nestin+/Sox2+). The NSCs were maintained in serum-free B27 medium in presence of 10 ng/ml FGF-2/bFGF (Peprotech) and 10 ng/ml EGF (Invitrogen). The monolayer cultures were serially passaged every 4-7 days. To avoid the potential non-specific effect induced by prolonged culturing, only NSCs with limited in vitro culturing (less than 3 weeks) were used in the study. J1 ESCs were maintained in standard culture conditions in presense of irradiated mouse embryonic fibroblasts.

extract_protocol: Each ChIP-chip assay was performed with about 20 million cells following Agilent mammalian ChIP-on-chip protocol (March, 2006). Briefly, cells were cross-linked with formaldehyde for 10 min at room temperature. Sonicated chromatin was immunoprecipitated overnight at 4 C with 10 ug immobilized (on 100 ul Dynal protein-G beads, Invitrogen) antibodies to Dnmt3a (Santa Cruz, sc-20703), H3K4me3 (Millipore, 07-473), H3K27me3 (Millipore, 07-449), total histone H3 (Millipore, 07-690), Ezh2 (Active Motif, 39103) and Suz12 (A kind gift from Dr. Yi Zhang). MeDIP-chip was perfromed as previously described with minor modifications (Weber et al., 2005). Briefly, 5 ug sonicated, heat-denatured genomic DNA was immunoprecipitated with 5 ul of monoclonal antibody against 5-methylcytidine (Eurogentec) at 4 C overnight. Immunoprecipitated methylated DNA was collected with 30 ul Dynal protein-G beads for 2 h at 4 C.

tag: genotype/variation

value: wild type

value: Postnatal day 14-21

value: embryonic stem cells

tag: experimental design

value: IP/WCE

source_name: WT ESC, immunoprecipitated DNA by H3K27me3 antibodies


title: CardiacMuscle_80mg/kgRosi_24hrs_rep2

value: Wistar


title: CardiacMuscle_80mg/kgRosi_24hrs_rep4


title: 01LKS

source_name: ERA

value: ERA


title: Dp310s line P4-18,biological rep1


title: 01N4P


title: 01LPH


title: CardiacMuscle_80mg/kgRosi_24hrs_rep5


title: Dm310s line M1-7,biological rep3

description: Expression data of Gal4/UAS-Dm310s larvae

source_name: progeny from the cross with maternal GAL4 line NP5941 and paternal UAS-dm310s line M1-7


title: WT embryonic stem cells (ESCs, J1), DNA methylatyion by MeDIP-chip (1/2), exp2

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_ESC_MeDIP_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT ESC, immunoprecipitated DNA by 5-methylcytosine antibodies


title: Dm310s line M1-7,biological rep2


title: WT embryonic stem cells (ESCs, J1), DNA methylatyion by MeDIP-chip (1/2), exp1


title: WT versus KO NSCs, H3K27me3 ChIP-chip (1/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WTvsKO_NSC_H3K27me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by H3K27me3 antibodies

value: neural stem cells

value: IP/IP

source_name: WT NSC, immunoprecipitated DNA by H3K27me3 antibodies


title: KO NSCs, Suz12 ChIP-chip (1/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: KO_NSC_Suz12_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, whole cell extract

source_name: KO NSC, immunoprecipitated DNA by Suz12 antibodies


title: WT versus KO NSCs, total histone H3 ChIP-chip (1/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WTvsKO_NSC_panH3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by total histone H3 antibodies

source_name: WT NSC, immunoprecipitated DNA by total histone H3 antibodies


title: CardiacMuscle_80mg/kgRosi_6hrs_rep5

source_name: Cardiac muscle sampled 6 hrs post 80 mg/kgrosiglitazone once daily for 14 days


title: CardiacMuscle_80mg/kgRosi_6hrs_rep6


title: Dm310s line M1-3,biological rep3

source_name: progeny from the cross with maternal GAL4 line NP5941 and paternal UAS-dm310s line M1-3


title: Dm310s line M1-7,biological rep1


title: Dm310s line M1-3,biological rep2


title: CardiacMuscle_80mg/kgRosi_6hrs_rep2


title: Dm310s line M1-3,biological rep1


title: WT versus KO NSCs, H3K4me3 ChIP-chip (1/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WTvsKO_NSC_H3K4me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by H3K4me3 antibodies

source_name: WT NSC, immunoprecipitated DNA by H3K4me3 antibodies


title: CardiacMuscle_80mg/kgRosi_6hrs_rep4


title: KO NSCs, Ezh2 ChIP-chip (1/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: KO_NSC_Ezh2_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by Ezh2 antibodies


title: CardiacMuscle_80mg/kgRosi_6hrs_rep1


title: WT NSCs, H3K27me3 ChIP-chip (1/2), exp2

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_H3K27me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT NSC, whole cell extract


title: WT NSCs, Ezh2 ChIP-chip (1/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_Ezh2_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT NSC, immunoprecipitated DNA by Ezh2 antibodies


title: WT versus KO NSCs, DNA methylatyion by MeDIP-chip (1/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WTvsKO_NSC_MeDIP_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by 5-methylcytosine antibodies

source_name: WT NSC, immunoprecipitated DNA by 5-methylcytosine antibodies


title: CardiacMuscle_10mg/kgRosi_336hrs_rep6

source_name: Cardiac muscle sampled 336 hrs post 10 mg/kg rosiglitazone once daily for 14 days


title: KO NSCs, H3K4me3 ChIP-chip (1/2), exp2

data_processing:
Final processed data file by ChIP Analytics 1.3: KO_NSC_H3K4me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.


title: KO NSCs, H3K4me3 ChIP-chip (1/2), exp1


title: WT NSCs, H3K4me3 ChIP-chip (1/2), exp2

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_H3K4me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.


title: CardiacMuscle_10mg/kgRosi_336hrs_rep5


title: WT NSCs, H3K27me3 ChIP-chip (1/2), exp1


title: CardiacMuscle_10mg/kgRosi_336hrs_rep4


title: WT NSCs, Suz12 ChIP-chip (1/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_Suz12_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT NSC, immunoprecipitated DNA by Suz12 antibodies


title: WT NSCs, H3K4me3 ChIP-chip (1/2), exp1


title: WT NSCs, DNA methylatyion by MeDIP-chip (1/2), exp3_1-week

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_MeDIP_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.


title: KO NSCs, H3K27me3 ChIP-chip (1/2), exp1

data_processing:
Final processed data file by ChIP Analytics 1.3: KO_NSC_H3K27me3_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, immunoprecipitated DNA by H3K27me3 antibodies


title: Cord blood CD4+_control siRNA_Act+IL-4_72h_rep3

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

hyb_protocol: 1.5 ug each sample was hybridized to Illumina’s Sentrix HumanWG-6 Expression BeadChips, version 2 (cat no BD-25-112) at 55C overnight (18½ h) according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A. Hybridization was detected with 1 ug/ml Cyanine3-streptavidin, Amersham Biosciences (cat no 146065).

scan_protocol: Chips were scanned with Illumina BeadArray Reader. The numerical results were extracted with GenomeStudio v1.0 without any normalization.

data_processing: The data were quantile-normalized using the R/Bioconductor package affy and log2-transformed.

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated, 72h

label_protocol: Amplification was started using 100ng total RNA with Ambion's Illumina RNA TotalPrep Amplification kit (cat no AMIL1791).  IVT reaction took overnight (14h) and during it cRNA was biotinylated. Both before and after the amplifications the RNA/cRNA concentrations where checked with Nanodrop ND-1000 and RNA/cRNA quality was controlled by BioRad’s Experion electrophoresis station.

growth_protocol: Umbilical cord blood was collected from healthy neonates born in Turku University Hospital, Hospital District of Southwest Finland. Mononuclear cells were isolated with Ficoll-Paque (Amersham Biosciences) gradient centrifugation, and CD4+ cell population was purified using magnetic beads (Dynal CD4 Positive Isolation Kit, Invitrogen) according to manufacturer's instructions.

extract_protocol: Total RNA was extracted with RNeasy mini kit (Qiagen) according to manufacturer's instructions. In-column DNase (RNase-Free DNase Set, Qiagen) treatment was performed for 15 minutes. RNA was eluted in dH2O.

treatment_protocol: siRNA mediated knockdowns were perfomed using Nucleofector (Amaxa Biosystems) with a method described elsewhere (Tahvanainen et al. J Immunol Methods. 2006 Mar 20;310(1-2):30-9.). STAT6 siRNA #1 (5´- AAGCAGGAAGAACTGAAGTTT- 3`) or control siRNA (5´-GCGCGCTTTGTAGGATTCG-3´) was introduced into the cells. Cells were rested for 24 h and then activated throught the T cell receptor (plate bound antiCD3 500 ng/24-well, and soluble antiCD28 500 ng/ml, Immunotech, France). Th2 polarization was initiated with IL-4 (10ng/ml, R&D Systems). Cells were cultured in Yssel´s medium. At 48h, IL-2 was added to the cultures (17ng/ml, R&D Systems). Cells were harvested after 12, 24, 48 or 72 h of polarization.

value: cord blood

value: CD4+ T cells

tag: genome/variation

value: Control siRNA

tag: biological replicate


title: WT NSCs, DNA methylatyion by MeDIP-chip (1/2), exp2_3-week


title: Cord blood CD4+_control siRNA_Act_72h_rep3

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 72h


title: CardiacMuscle_10mg/kgRosi_336hrs_rep3

data_processing: GCOS software using MAS5


title: WT NSCs, Dnmt3a ChIP-chip (1/2), exp2

data_processing:
Final processed data file by ChIP Analytics 1.3: WT_NSC_Dnmt3a_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: WT NSC, immunoprecipitated DNA by Dnmt3a antibodies


title: Cord blood CD4+_control siRNA_Act+IL-4_48h_rep3

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated, 48h


title: Normal B Cell Control 10 Jel108U133B

data_processing: Affymetrix GeneChip® Operating System software v.1.3 (Santa Clara, CA) were used to quantitatively analyze the scanned image

source_name: Purified B cells from peripheral blood from donors 60 years of age and older

tag: disease state

value: normal


title: CardiacMuscle_10mg/kgRosi_336hrs_rep1


title: Chronic Lymphocytic Leukemia (CLL) sample 41 Jel107U133B

source_name: Purified CLL B cells from peripheral blood

value: CLL

tag: cell type


title: CardiacMuscle_10mg/kgRosi_336hrs_rep2


title: KO NSCs, Dnmt3a ChIP-chip (1/2)

data_processing:
Final processed data file by ChIP Analytics 1.3: KO_NSC_Dnmt3a_mm7_log2ratio.txt

Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing (VALUE providide in the Sample table below: log2 (Cy5_Signal/Cy3_Signal)). FE files (.txt) was subsequently analyzed using ChIP analytics 1.3 (Agilent). For IP/WCE experiments, we performed blank subtraction normalization, inter-array median normalization and intra-array median normalization by calculating a one-step Tukey biweight median. For IP/IP experiments, we performed an intra-array Lowess normalization. Replicate experiments were combined in ChIP analytics 1.3 (Agilent) to generate a weighted log2ratio for peak detection.

ChIP analytics data are provided as supplementary files on the Series record.  The first three columns in the files represent genome coordinates (mm7) of all data probes with signals above the background threshold.  The fourth column is the normalized log2 (Cy5_signal/Cy3_signal) for the corresponding probe calculated by ChIP Analytics.  When replicate experiments available, the fourth column represents a weighted log2 ration from multiple experiments.

source_name: KO NSC, whole cell extract

source_name: KO NSC, immunoprecipitated DNA by Dnmt3a antibodies


title: Cord blood CD4+_control siRNA_Act+IL-4_24h_rep3

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated, 24h


title: Cord blood CD4+_control siRNA_Act_12h_rep3

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 12h


title: Normal B Cell Control 11 Jel109U133B

value: Purified B cells from peripheral blood from donors 60 years of age and older


title: Cord blood CD4+_control siRNA_0h_rep3

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, 0h


title: WT NSCs, Dnmt3a ChIP-chip (1/2), exp1

source_name: WT NSC, whole cell extract


title: Cord blood CD4+_control siRNA_Act+IL-4_12h_rep3

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated,12h


title: Chronic Lymphocytic Leukemia (CLL) sample 39 Jel105U133B

value: Purified CLL B cells from peripheral blood


title: CardiacMuscle_10mg/kgRosi_168hrs_rep6

source_name: Cardiac muscle sampled 168 hrs post 10 mg/kg rosiglitazone once daily for 14 days

value: male


title: Chronic Lymphocytic Leukemia (CLL) sample 40 Jel106U133B


title: Cord blood CD4+_control siRNA_Act_48h_rep3

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 48h


title: Cord blood CD4+_control siRNA_Act_24h_rep3

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 24h


title: Array CGH data for breast cancer cell line T47D

city: Helsinki

first: Henrik

last: Edgren

address: Tukholmankatu 8

institute: Institute for Molecular Medicine, University of Helsinki

description: A hybridization of untreated T47D human breast cancer cells compared to normal human female genomic DNA.

hyb_protocol: Labelled tumor and reference samples were combined and hybridized onto the arrays according to the direct method of the June 2006, version 4 protocol (Agilent Technologies, Palo Alto, CA). After hybridization, arrays were washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned using the G2505B scanner from Agilent Technologies. Signal intensities were quantified using the Feature Extraction software from Agilent.

data_processing: Agilent Feature Extraction Software version 9.1.1.1 was used for spot quality filtering and normalization using default settings.

source_name: normal female reference DNA

label_protocol: Six micrograms of digested and purified DNA was labelled with Cy3-dUTP in a random priming reaction using BioPrime DNA Labelling System.

extract_protocol: Genomic DNA was extracted from untreated cells using the NucleoSpin Tissue kit with the protocol for cultured cells.

tag: reference

value: Normal female reference genomic DNA (Promega)

source_name: breast cancer cell line T47D

label_protocol: Six micrograms of digested and purified DNA was labelled with Cy5-dUTP in a random priming reaction using BioPrime DNA Labelling System.

growth_protocol: Cell cultures were grown to 70-80% confluence in 175 cm2 flasks according to distributor's instructions (ATCC).

value: breast cancer cell line

tag: cell line


title: Cord blood CD4+_STAT6 siRNA_Act_72h_rep3

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 72h

tag: tissue

value: STAT6 siRNA


title: Cord blood CD4+_STAT6 siRNA_Act+IL-4_72h_rep3

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated, 72h


title: Chronic Lymphocytic Leukemia (CLL) sample 38 Jel104U133B


title: WT vs KO differentiated NSCs, Replicate 2

description: Biological replicate 2 of 2. Differentiated NSCs harvested after 3 days of mitogen withdrawal.

hyb_protocol: 825 ng Cy3- or Cy5-labelled cRNA were combined and hybridized to the Agilent 4x44K mouse whole genome microarray (G4122F) for 17 h at 65 ˚C (10 r.p.m.). Microarrays were washed according to Agilent's standard procedures.

data_processing: Agilent Feature Extraction (FE) Software (v 9.5) was used for tiff image processing, background subtraction and Lowess normalization. Normalized signal intensity from FE was used for identifying differentially expressed transcripts between WT and KO NSCs in NIA array analysis tool (http://igsun.grc.nia.nih.gov/ANOVA).

source_name: WT NSCs

label_protocol: 500 ng of total RNA from WT and KO NSCs was reversed transcribed and labeled with Cy3- or Cy5-CTP using the Agilent Low RNA Input Fluorescent Linear Amplification Kit respectively.

growth_protocol: Postnatal day 14-21 day mouse lateral ventricle walls were dissected and mechanically dissociated. Single cell suspensions were plated at low density (10,000~20,000 cells cm-2) on cell culture dishes coated with poly-L-ornithine (PO)/fibronectin (FN), allowing individual cells to form spatially distinct colonies. Serial passage (less than 2 passages, or 2 weeks) allowed us to enrich undifferentiated NSCs to high purity (>95% Nestin+/Sox2+). The NSCs were maintained in serum-free B27 medium in presence of 10 ng/ml FGF-2/bFGF (Peprotech) and 10 ng/ml EGF (Invitrogen). The monolayer cultures were serially passaged every 4-7 days. To avoid the potential non-specific effect induced by culture adaption, only NSCs with limited in vitro culturing (less than 3 weeks) were used in the study.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: For spontaneous neuronal and glial differentiation, a cohort of undifferentiated NSCs, were re-plated on PO/FN substrate with mitogen for 2 days followed by withdrawal of mitogens for an additional 3 days.

value: wild type

value: Postnatal day 14-21

value: subventricular zones

source_name: KO NSCs


title: Cord blood CD4+_STAT6 siRNA_Act_48h_rep3

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 48h


title: CardiacMuscle_10mg/kgRosi_168hrs_rep4

value: Wistar

tag: gender


title: CardiacMuscle_10mg/kgRosi_168hrs_rep2


title: Cord blood CD4+_STAT6_siRNA_Act+IL-4_48h_rep3

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated, 48h


title: Chronic Lymphocytic Leukemia (CLL) sample 37 Jel102U133B

description: Gene expression data from peripheral blood B cells from patients diagnosed with CLL prior to treatment

source_name: Purified CLL B cells from peripheral blood


title: WT vs KO differentiated NSCs, Replicate 1

description: Biological replicate 1 of 2. Differentiated NSCs harvested after 3 days of mitogen withdrawal.

value: neural stem cells


title: Cord blood CD4+_STAT6 siRNA_Act_24h_rep3

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 24h


title: Cord blood CD4+_STAT6 siRNA_Act+IL-4_12h_rep3

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated,12h


title: WT vs KO proliferating/undifferentiated NSCs, Replicate 3

description: Biological replicate 3 of 4. Undifferentiated/proliferating NSCs harvested after 2-3 passages.


title: CardiacMuscle_10mg/kgRosi_168hrs_rep3


title: Cord blood CD4+_STAT6 siRNA_Act_12h_rep3

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 12h


title: Cord blood CD4+_STAT6 siRNA_Act+IL-4_24h_rep3

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated, 24h


title: CardiacMuscle_10mg/kgRosi_24hrs_rep6

source_name: Cardiac muscle sampled 24 hrs post 10 mg/kg rosiglitazone once daily for 14 days


title: Cord blood CD4+_STAT6 siRNA_0h_rep3

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, 0h


title: CardiacMuscle_10mg/kgRosi_24hrs_rep2


title: WT vs KO proliferating/undifferentiated NSCs, Replicate 4

description: Biological replicate 4 of 4. Undifferentiated/proliferating NSCs harvested after 2-3 passages.


title: Chronic Lymphocytic Leukemia (CLL) sample 36 Jel101U133B


title: Normal B Cell Control 8 Jel066U133B

description: Gene expression data from peripheral blood  B cells age matched normal controls

source_name: Purified B cells from peripheral blood from donors 60 years of age and older


title: Chronic Lymphocytic Leukemia (CLL) sample 34 Jel065U133B


title: WT vs KO proliferating/undifferentiated NSCs, Replicate 1

description: Biological replicate 1 of 4. Undifferentiated/proliferating NSCs harvested after 2-3 passages.


title: CardiacMuscle_10mg/kgRosi_24hrs_rep3


title: Normal B Cell Control 9 Jel100U133B


title: Chronic Lymphocytic Leukemia (CLL) sample 35 Jel067U133B


title: MDA/pre-miR-125b vs. MDA/pre-control

first: Li

middle: Xu

last: Yan

address: 651# Dong Feng Road East

department: Department of Pathology

institute: Sun Yat-Sen University Cancer Center

description: compare gene expression profiles of pre-miR-125b transfected MDA-MB-231 cells with pre-control transfected MDA-MB-435 cells

hyb_protocol: Standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed.

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Cells were maintained in Dulbecco's modified Eagle's medium, supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin and 10% fetal bovine serum (GIBCO-Invitrogen, California, USA).

extract_protocol: Total RNA was isolated 24 h post-transfection, using Trizol reagent (Invitrogen).

treatment_protocol: the pre-miR-125b (Ambion, USA) were delivered at a final concentration of 25 nmol/L using Lipofectamine 2000 reagent (Invitrogen).

value: MDA-MB-435 transfected with pre-miR-125b

value: breast cancer MDA-MB-435, a metastatic breast cancer cell line

source_name: MDA/pre-control

treatment_protocol: the pre-control (Ambion, USA) were delivered at a final concentration of 25 nmol/L using Lipofectamine 2000 reagent (Invitrogen).

value: MDA-MB-435 transfected with pre-control


title: Chronic Lymphocytic Leukemia (CLL) sample 31 Jel060U133B


title: CardiacMuscle_10mg/kgRosi_6hrs_rep5

source_name: Cardiac muscle sampled 6 hrs post 10 mg/kg rosiglitazone once daily for 14 days


title: CardiacMuscle_10mg/kgRosi_24hrs_rep5


title: CardiacMuscle_10mg/kgRosi_6hrs_rep4


title: Chronic Lymphocytic Leukemia (CLL) sample 33 Jel064U133B


title: WT NSCs, DNA methylatyion by MeDIP-chip (1/2), exp1_3-week

source_name: WT NSC, whole cell extract

value: IP/WCE

source_name: WT NSC, immunoprecipitated DNA by 5-methylcytosine antibodies


title: Cord blood CD4+_control siRNA_Act+IL-4_72h_rep2

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated, 72h

value: cord blood

value: CD4+ T cells

value: Control siRNA


title: Chronic Lymphocytic Leukemia (CLL) sample 30 Jel058U133B

value: CLL

value: Purified CLL B cells from peripheral blood


title: Cord blood CD4+_control siRNA_Act_72h_rep2

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 72h


title: CardiacMuscle_10mg/kgRosi_168hrs_rep5

source_name: Cardiac muscle sampled 168 hrs post 10 mg/kg rosiglitazone once daily for 14 days

value: male


title: WT vs KO proliferating/undifferentiated NSCs, Replicate 2

description: Biological replicate 2 of 4. Undifferentiated/proliferating NSCs harvested after 2-3 passages.

source_name: KO NSCs

source_name: WT NSCs


title: MCF/pre-miR-125b vs. MCF/pre-control

description: compare gene expression profiles of pre-miR-125b transfected MCF-7 cells with pre-control transfected MCF-7 cells

extract_protocol: Total RNA was isolated 12 h post-transfection, using Trizol reagent (Invitrogen).

value: MCF-7 transfected with pre-miR-125b

value: breast cancer MCF-7, retained several characteristics of differentiated mammary epithelium

source_name: MCF/pre-control

value: MCF-7 transfected with pre-control


title: Cord blood CD4+_control siRNA_Act+IL-4_48h_rep2

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated, 48h


title: CardiacMuscle_10mg/kgRosi_24hrs_rep1


title: CardiacMuscle_10mg/kgRosi_6hrs_rep2


title: Cord blood CD4+_control siRNA_Act+IL-4_24h_rep2

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated, 24h


title: CardiacMuscle_10mg/kgRosi_6hrs_rep1


title: CardiacMuscle_10mg/kgRosi_6hrs_rep3


title: Cord blood CD4+_control siRNA_Act_48h_rep2

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 48h


title: CardiacMuscle_Vehicle_336hrs_rep6

source_name: Cardiac muscle sampled 336 hrs post Vehicle Treatment once daily for 14 days


title: Chronic Lymphocytic Leukemia (CLL) sample 28 Jel056U133B

source_name: Purified CLL B cells from peripheral blood


title: Cord blood CD4+_control siRNA_Act+IL-4_12h_rep2

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated,12h


title: Cord blood CD4+_control siRNA_Act_24h_rep2

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 24h


title: Chronic Lymphocytic Leukemia (CLL) sample 26 Jel052B


title: Chronic Lymphocytic Leukemia (CLL) sample 27 Jel054B


title: Chronic Lymphocytic Leukemia (CLL) sample 29 Jel057U133B


title: CardiacMuscle_Vehicle_336hrs_rep5


title: Chronic Lymphocytic Leukemia (CLL) sample 25 Jel051B


title: Normal B Cell Control 7 Jel055B

source_name: Purified B cells from peripheral blood from donors 60 years of age and older

value: normal


title: CardiacMuscle_Vehicle_336hrs_rep4


title: CardiacMuscle_Vehicle_336hrs_rep2


title: Cord blood CD4+_control siRNA_0h_rep2

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, 0h


title: Cord blood CD4+_control siRNA_Act_12h_rep2

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 12h


title: CardiacMuscle_Vehicle_336hrs_rep3


title: Cord blood CD4+_STAT6 siRNA_Act_72h_rep2

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 72h

value: STAT6 siRNA


title: Chronic Lymphocytic Leukemia (CLL) sample 24 Jel050B


title: Chronic Lymphocytic Leukemia (CLL) sample 23 Jel049B


title: Chronic Lymphocytic Leukemia (CLL) sample 22 Jel048B


title: CardiacMuscle_Vehicle_168hrs_rep4

source_name: Cardiac muscle sampled 168 hrs post Vehicle Treatment once daily for 14 days

value: Wistar


title: CardiacMuscle_Vehicle_168hrs_rep5


title: Cord blood CD4+_STAT6 siRNA_Act_48h_rep2

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 48h


title: Cord blood CD4+_STAT6_siRNA_Act+IL-4_48h_rep2

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated, 48h


title: Chronic Lymphocytic Leukemia (CLL) sample 32 Jel063U133B


title: CardiacMuscle_Vehicle_168hrs_rep3


title: Chronic Lymphocytic Leukemia (CLL) sample 21 Jel047B


title: Cord blood CD4+_STAT6 siRNA_Act+IL-4_24h_rep2

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated, 24h


title: Chronic Lymphocytic Leukemia (CLL) sample 20 Jel046B


title: CardiacMuscle_Vehicle_168hrs_rep2


title: Chronic Lymphocytic Leukemia (CLL) sample 19 Jel045B


title: Cord blood CD4+_STAT6 siRNA_Act+IL-4_72h_rep2

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated, 72h


title: CardiacMuscle_Vehicle_168hrs_rep1


title: Cord blood CD4+_STAT6 siRNA_Act_24h_rep2

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 24h


title: CardiacMuscle_Vehicle_24hrs_rep5

source_name: Cardiac muscle sampled 24 hrs post Vehicle Treatment once daily for 14 days


title: Chronic Lymphocytic Leukemia (CLL) sample 18 Jel044B


title: CardiacMuscle_Vehicle_24hrs_rep6


title: CardiacMuscle_Vehicle_24hrs_rep4


title: CardiacMuscle_Vehicle_24hrs_rep3


title: Cord blood CD4+_STAT6 siRNA_Act+IL-4_12h_rep2

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated,12h


title: Cord blood CD4+_STAT6 siRNA_Act_12h_rep2

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 12h


title: Chronic Lymphocytic Leukemia (CLL) sample 14 Jel039U133B


title: CardiacMuscle_Vehicle_24hrs_rep1


title: Cord blood CD4+_control siRNA_Act_72h_rep1

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 72h


title: CardiacMuscle_Vehicle_24hrs_rep2


title: Chronic Lymphocytic Leukemia (CLL) sample 17 Jel043B

source_name: Purified CLL B cells from peripheral blood


title: CardiacMuscle_Vehicle_6hrs_rep6

source_name: Cardiac muscle sampled 6 hrs post Vehicle Treatment once daily for 14 days


title: Chronic Lymphocytic Leukemia (CLL) sample 15 Jel040U133B


title: Cord blood CD4+_control siRNA_Act+IL-4_72h_rep1

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated, 72h


title: Cord blood CD4+_STAT6 siRNA_0h_rep2

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, 0h


title: Cord blood CD4+_control siRNA_Act_48h_rep1

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 48h


title: Chronic Lymphocytic Leukemia (CLL) sample 13 Jel038U133B


title: Cord blood CD4+_control siRNA_Act+IL-4_24h_rep1

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated, 24h


title: CardiacMuscle_Vehicle_6hrs_rep3


title: Normal B Cell Control 5 Jel037U133B

source_name: Purified B cells from peripheral blood from donors 60 years of age and older


title: Cord blood CD4+_control siRNA_Act+IL-4_48h_rep1

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated, 48h


title: Chronic Lymphocytic Leukemia (CLL) sample 16 Jel042B


title: Cord blood CD4+_control siRNA_Act_24h_rep1

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 24h


title: CardiacMuscle_Vehicle_6hrs_rep5


title: Cord blood CD4+_control siRNA_Act+IL-4_12h_rep1

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated and IL-4 treated,12h


title: Chronic Lymphocytic Leukemia (CLL) sample 12 Jel036U133B


title: Normal B Cell Control 4 Jel033U133B

value: Purified B cells from peripheral blood from donors 60 years of age and older


title: Cord blood CD4+_control siRNA_Act_12h_rep1

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, activated, 12h


title: Chronic Lymphocytic Leukemia (CLL) sample 11 Jel032U133B


title: CardiacMuscle_Vehicle_6hrs_rep1


title: Cord blood CD4+_control siRNA_0h_rep1

source_name: human cord blood CD4+ cell, nucleofected with control siRNA, 0h


title: Chronic Lymphocytic Leukemia (CLL) sample 10 Jel031U133B


title: Cord blood CD4+_STAT6 siRNA_Act+IL-4_72h_rep1

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated, 72h


title: Chronic Lymphocytic Leukemia (CLL) sample 9 Jel030U133B


title: Cord blood CD4+_STAT6 siRNA_Act_72h_rep1

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 72h


title: Dp310 vs. w1118 (dye-swap)

description: dye swap, GAL4/UAS-Dp310s larvae vs GLA4/w1118 larvae

hyb_protocol: Following the Dendrimer Use and Hybridization Protocol (Cherbas 2006) from CGB Technical Report 2006-08

scan_protocol: Scanned on an  GenePix 4000B microarray scanner. Images were quantified using Genepix Pro. 6.

data_processing: Raw data of cDNA arrays were normalized using within array print-tip loess normalization and between arrays quantile normalization as implemented in the BioConductor package limma

source_name: progeny from the cross with maternal NP5941 and paternal w1118

value: third-instar larvae

source_name: progeny from the cross with maternal NP5941 and paternal UAS-dp310s


title: Dm310 vs. w1118 (dye-swap)

description: dye swap, GAL4/UAS-Dm310s larvae vs GLA4/w1118 larvae

label_protocol: Following the Dendrimer Use and Hybridization Protocol (Cherbas 2006) from CGB Technical Report 2006-08

source_name: progeny from the cross with maternal NP5941 and paternal UAS-dm310s


title: Dp310 vs. Dm310

description: GLA4/UAS-Dp310s larvae vs. GLA4/UAS-Dm310s larvae


title: Normal B Cell Control 3 Jel028U133B


title: Dp310 vs. Dm310 (dye-swap)

description: dye swap, GLA4/UAS-Dp310s larvae vs. GLA4/UAS-Dm310s larvae


title: Cord blood CD4+_STAT6_siRNA_Act+IL-4_48h_rep1

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated, 48h


title: Dp310 vs. w1118

description: GAL4/UAS-Dp310s larvae vs GLA4/w1118 larvae


title: Dm310 vs. w1118

description: GAL4/UAS-Dm310s larvae vs GLA4/w1118 larvae


title: Cord blood CD4+_STAT6 siRNA_Act_48h_rep1

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 48h


title: Chronic Lymphocytic Leukemia (CLL) sample 7 Jel026U133B

source_name: Purified CLL B cells from peripheral blood


title: Chronic Lymphocytic Leukemia (CLL) sample 8 Jel027U133B


title: Chronic Lymphocytic Leukemia (CLL) sample 5 Jel023U133B


title: Chronic Lymphocytic Leukemia (CLL) sample 6 Jel025U133B


title: Cord blood CD4+_STAT6 siRNA_Act+IL-4_24h_rep1

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated, 24h


title: Cord blood CD4+_STAT6 siRNA_Act+IL-4_12h_rep1

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated and IL-4 treated,12h


title: Cord blood CD4+_STAT6 siRNA_Act_24h_rep1

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 24h


title: Normal B Cell Control 2 Jel024U133B

source_name: Purified B cells from peripheral blood from donors 60 years of age and older


title: Cord blood CD4+_STAT6 siRNA_0h_rep1

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, 0h


title: Chronic Lymphocytic Leukemia (CLL) sample 4 Jel022U133B


title: Chronic Lymphocytic Leukemia (CLL) sample 2 Jel019U133B


title: Chronic Lymphocytic Leukemia (CLL) sample 3 Jel021U133B


title: Cord blood CD4+_STAT6 siRNA_Act_12h_rep1

source_name: human cord blood CD4+ cell, nucleofected with STAT6 siRNA, activated, 12h


title: Chronic Lymphocytic Leukemia (CLL) sample 1 Jel018U133B


title: Normal B Cell Control 1 Jel020U133B


title: Normal B Cell Control 6 Jel041U133B


title: TAX577048

status: Public on Jun 24 2010

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: BAC aCGH microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if either: (1) flagged during image-analysis, (2) background corrected intensity value >64999 signal units, (3) background corrected intensity value <0 signal units, or (4) Signal to noise ratio <5 in either Int1 or Int2 channel. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying popLowess (PMID: 17953745). Spots from dye-swap hybridization were merged using geometric mean of ratios after normalization.

source_name: Breast tumor

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions using the Invitrogen Bioprime aCGH Genomic Labeling Module as described (PMID:17334996).

extract_protocol: Genomic DNA from fresh frozen breast tumor tissue was extracted using overnight digestion with proteinase K at 55C, followed by repeated phenol-chloroform purification steps. DNA concentrations were measured using a Nanodrop.

value: Breast tumor

tag: hu subtype

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: genomic subtype

source_name: promega male reference

value: promega male reference


title: TAX577576

value: LumA

value: amplifier


title: TAX577047


title: TAX577111


title: TAX577117

value: Luminal-complex


title: TAX577216

value: Luminal-simple


title: TAX577290

value: Normal

value: sporadic


title: TAX577377

value: Basal

value: Basal-complex


title: TAX577088


title: TAX577408


title: TAX577495


title: TAX577061


title: TAX577072

value: LumB


title: TAX577064

value: nonClassified


title: TAX577490


title: TAX577541


title: WTvsKO NSCs, DNA methylation by MeDIP-chip (3/4), exp2

hyb_protocol: 34 ug of Cy5- and Cy3-labeled samples were combined and hybridized to each mouse whole genome tiling microarray (Roche/NimbleGen 4-array set) for 16-20 h at 42 ˚C using NimbleGen hybridization System 4.

scan_protocol: Microarrays were scanned using the Agilent scanner at 5 micron resolution.

data_processing:
Data were extracted and analyzed using NimbleScan v2.5 (Roche/NimbleGen). Dnmt3a binding sites were identified by a sliding window-base statistical algorithm in NimbleScan v2.5 (FDR<1% or <5%). For identifying probes associated with a significant increase in H3K27me3 levels or a significant decrease in DNA methylation level in KO NSCs as compared to WT NSCs, a non-parametric one-sided Kolmogorov-Smirno (KS) test was used (KS score>2).
Processed data VALUE definition: Log2 (ch2_signal / ch1_signal)

source_name: KO NSC, immunoprecipitated DNA by 5-methylcytosine antibodies

label_protocol: Whole cell extract and immunoprecipitated DNA were amplified using the Whole Genome Amplification Kit (Sigma), and 5 ug of amplified ChIP/MeDIP or input samples were labeled (5’ Cy5- or Cy3-random nonamers, TriLink Biotechnologies) using the standard protocol (NimbleGen Arrays User’s Guide for ChIP-chip analysis).

growth_protocol: postnatal SVZ NSCs were maintained in undifferentiated states in presence of mitogens (10 ng/ml EGF and 10 ng/ml bFGF)

extract_protocol: Each ChIP-chip assay was performed with about 20 million cells following Agilent mammalian ChIP-on-chip protocol (March, 2006). Briefly, cells were cross-linked with formaldehyde for 10 min at room temperature. Sonicated chromatin was immunoprecipitated overnight at 4 C with 10 ug immobilized (on 100 ul Dynal protein-G beads, Invitrogen) antibodies to Dnmt3a (Santa Cruz, sc-20703) or H3K27me3 (Millipore, 07-449). MeDIP-chip was perfromed as previously described with minor modifications (Weber et al., 2005). Briefly, 5 ug sonicated, heat-denatured genomic DNA was immunoprecipitated with 5 ul of monoclonal antibody against 5-methylcytidine (Eurogentec) at 4 C overnight. Immunoprecipitated methylated DNA was collected with 30 ul Dynal protein-G beads for 2 h at 4 C.

value: postnatal SVZ

tag: genotype/variation

value: neural stem cells

tag: experimental design

value: IP/IP

source_name: WT NSC, immunoprecipitated DNA by 5-methylcytosine antibodies

value: wild type


title: TAX577184

value: Breast tumor


title: TAX577183

description:
raw data file TAX577183_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577183_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5

value: familial


title: TAX577360

value: promega male reference


title: TAX577550


title: TAX577330


title: TAX577368


title: TAX577122

value: LumA


title: TAX577193


title: WTvsKO NSCs, DNA methylation by MeDIP-chip (3/4), exp1


title: TAX577053


title: TAX577076


title: TAX577013


title: TAX577372


title: TAX577191


title: TAX577274

value: mixed


title: TAX577379


title: TAX577430

value: amplifier


title: WT NSCs, Dnmt3a ChIP-chip (3/4)

source_name: WT NSC, whole cell extract

value: IP/WCE

source_name: WT NSC, immunoprecipitated DNA by Dnmt3a antibodies


title: WTvsKO NSCs, H3K27me3 ChIP-chip (3/4)

source_name: WT NSC, immunoprecipitated DNA by H327me3 antibodies

source_name: KO NSC, immunoprecipitated DNA by H327me3 antibodies


title: TAX577456

value: Luminal-complex


title: TAX577009


title: TAX577237


title: TAX577364


title: TAX577304

value: Normal

value: sporadic


title: TAX577057


title: TAX577439


title: TAX577022

value: Basal


title: TAX577010

description:
raw data file TAX577010_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577010_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5


title: TAX577268

value: Luminal-simple


title: TAX577417


title: TAX577524


title: TAX577207

value: LumB


title: TAX577042

description:
raw data file TAX577042_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577042_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5


title: TAX577055

value: nonClassified


title: TAX577043


title: TAX577034


title: WT NSCs, Dnmt3a ChIP-chip (4/4)

value: postnatal SVZ

value: neural stem cells


title: TAX577329

value: Basal-complex


title: TAX577087

value: Breast tumor


title: TAX577444

value: familial


title: TAX577045

value: promega male reference


title: TAX577287


title: WTvsKO NSCs, H3K27me3 ChIP-chip (4/4)

value: wild type

value: IP/IP


title: TAX577044


title: TAX577284


title: WTvsKO NSCs, H3K27me3 ChIP-chip (2/4)


title: TAX577068

value: LumA


title: TAX577014


title: TAX577285

value: amplifier


title: WTvsKO NSCs, DNA methylation by MeDIP-chip (2/4), exp1


title: TAX577033


title: TAX577015


title: TAX577052


title: TAX577279

value: Luminal-complex


title: TAX577358


title: WT NSCs, Dnmt3a ChIP-chip (2/4)

value: IP/WCE


title: TAX577174


title: TAX577166

value: sporadic


title: TAX577253


title: TAX577575

value: Basal

value: mixed


title: TAX577302


title: TAX577136


title: TAX577449


title: TAX577011

value: LumB


title: WTvsKO NSCs, DNA methylation by MeDIP-chip (4/4), exp2


title: TAX577386


title: TAX577049


title: TAX577505

description:
raw data file TAX577505_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577505_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5


title: TAX577145


title: WTvsKO NSCs, DNA methylation by MeDIP-chip (2/4), exp2


title: TAX577345


title: TAX577359


title: TAX577325

value: nonClassified


title: TAX577338


title: TAX577221

value: Luminal-simple


title: WTvsKO NSCs, DNA methylation by MeDIP-chip (4/4), exp1

value: postnatal SVZ

value: neural stem cells


title: TAX577236

value: Breast tumor


title: TAX577235


title: TAX577574


title: TAX577555

value: familial


title: TAX577128

value: promega male reference


title: TAX577261


title: TAX577172


title: TAX577461


title: TAX577263

value: Normal

value: Basal-complex


title: TAX577040


title: TAX577242


title: TAX577001


title: TAX577286

value: LumA


title: TAX577164


title: TAX577226


title: TAX577539

value: amplifier


title: TAX577303


title: TAX577230

value: Luminal-complex


title: TAX577008


title: TAX577179


title: TAX577139


title: TAX577353


title: TAX577305


title: TAX577125


title: TAX577225


title: TAX577367


title: TAX577352


title: TAX577066

description:
raw data file TAX577066_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577066_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5


title: TAX577201


title: TAX577005


title: TAX577219


title: TAX577171


title: TAX577129


title: TAX577060


title: TAX577170


title: TAX577062


title: TAX577538

description:
raw data file TAX577538_Cy5_1.gpr is labeled as follows: ch1 = Cy5, ch2 = Cy3
raw data file TAX577538_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577538_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5


title: TAX577038


title: TAX577107


title: TAX577070


title: TAX577031


title: TAX577453


title: TAX577196


title: TAX577189


title: TAX577203


title: TAX577314


title: TAX577570


title: TAX577351


title: TAX577289


title: TAX577577


title: Prostate normal PAN0174 miRNA

city: New York

first: Barry

middle: Stephen

last: Taylor

state: NY

address: 1275 York Avenue, Box #460

institute: Memorial Sloan-Kettering Cancer Center

description: microRNA expression profiling

hyb_protocol: Per manufacturer's instructions

scan_protocol: Per manufacturer's instructions

data_processing: Images were quantified using Agilent Feature Extraction version 9.5 and data was normalized with between-array variance stabilization normalization (VSN) after excluding any microRNA not present in >80% of the samples profiled

source_name: human adjacent normal prostate

label_protocol: 200ng of total RNA was labeled using the miRNA Complete Labeling and Hybridization Kit (Agilent)

extract_protocol: Total RNA was isolaged using TRIzol@Reagent Total RNA Isoloation (Invitrogen), quantified with Thermo Scientific NanoDrop 1000 Spectrophotometer, and quality controlled with RNA 6000 picoAssay and Bioanalyzer 2100 (Agilent).

tag: sample id

value: Prostate

tag: disease status

value: normal adjacent benign prostate


title: Prostate normal PAN0162 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0169 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0171 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0144 miRNA

description: microRNA expression profiling


title: TAX577113

value: sporadic

tag: reference


title: TAX577194


title: TAX577395

value: Basal


title: Prostate normal PAN0136 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0135 miRNA

description: microRNA expression profiling


title: TAX577153


title: Prostate normal PAN0134 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0172 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0167 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0128 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0129 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0147 miRNA

description: microRNA expression profiling


title: TAX577205


title: Prostate normal PAN0127 miRNA

description: microRNA expression profiling


title: TAX577297


title: TAX577503

value: LumB


title: TAX577012


title: TAX577198


title: TAX577182


title: TAX577231


title: Prostate normal PAN0120 miRNA

description: microRNA expression profiling


title: TAX577208


title: Prostate normal PAN0122 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0125 miRNA

description: microRNA expression profiling


title: TAX577234


title: Prostate normal PAN0115 miRNA

description: microRNA expression profiling


title: TAX577209


title: TAX577300


title: TAX577212


title: TAX577569


title: TAX577422


title: Prostate normal PAN0114 miRNA

description: microRNA expression profiling


title: TAX577350


title: Prostate normal PAN0112 miRNA

description: microRNA expression profiling


title: TAX577133

value: mixed


title: Prostate normal PAN0117 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0109 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0110 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0164 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0107 miRNA

description: microRNA expression profiling


title: Prostate normal PAN0113 miRNA

description: microRNA expression profiling


title: TAX577526

description:
raw data file TAX577526_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577526_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5


title: Cell line Vcap miRNA

description: microRNA expression profiling

source_name: human prostate cancer cell line

value: Vcap

tag: cell type

value: prostate cancer cell line

tag: cell line


title: Prostate normal PAN0151 miRNA

description: microRNA expression profiling

tag: tissue


title: Prostate normal PAN0157 miRNA

description: microRNA expression profiling


title: TAX577173

tag: hu subtype


title: TAX577571

value: nonClassified

tag: familial status


title: TAX577448

value: Breast tumor

tag: er


title: TAX577275

tag: osbin


title: TAX577214

description:
raw data file TAX577214_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577214_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5

tag: os


title: TAX577104

value: familial

tag: pgr


title: TAX577243

value: promega male reference


title: TAX577181


title: Prostate tumor PCA0207 miRNA

description: microRNA expression profiling

source_name: human prostate

value: prostate cancer

tag: tumor type

value: Metastasis


title: Prostate tumor PCA0206 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0213 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0203 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0201 miRNA

description: microRNA expression profiling


title: TAX577556

tag: grade


title: Prostate tumor PCA0200 miRNA

description: microRNA expression profiling


title: TAX577511

value: LumA

tag: genomic subtype


title: TAX577425

value: Basal-complex


title: TAX577478

value: amplifier


title: TAX577433

value: Luminal-complex


title: TAX577195


title: Prostate tumor PCA0211 miRNA

description: microRNA expression profiling

value: Prostate


title: TAX577016

value: sporadic


title: Prostate tumor PCA0208 miRNA

description: microRNA expression profiling


title: TAX577306


title: TAX577394

value: Basal


title: TAX577497


title: TAX577223


title: TAX577479


title: TAX577187

value: LumB


title: Prostate tumor PCA0173 miRNA

description: microRNA expression profiling

value: Primary tumor


title: Prostate tumor PCA0172 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0175 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0174 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0179 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0180 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0181 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0178 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0184 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0194 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0189 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0187 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0199 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0190 miRNA

description: microRNA expression profiling


title: TAX577438

value: Normal


title: TAX577447


title: Prostate tumor PCA0170 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0171 miRNA

description: microRNA expression profiling


title: TAX577442


title: TAX577197


title: TAX577151


title: TAX577220

value: Luminal-simple


title: TAX577376


title: TAX577529


title: Prostate tumor PCA0168 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0164 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0165 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0167 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0169 miRNA

description: microRNA expression profiling


title: TAX577112


title: TAX577039

value: mixed


title: Prostate tumor PCA0162 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0161 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0160 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0159 miRNA

description: microRNA expression profiling


title: TAX577472

value: Breast tumor

value: nonClassified


title: TAX577542

description:
raw data file TAX577542_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577542_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5

value: promega male reference


title: TAX577572


title: Prostate tumor PCA0163 miRNA

description: microRNA expression profiling

value: prostate cancer


title: Prostate tumor PCA0158 miRNA

description: microRNA expression profiling


title: TAX577454

value: familial


title: TAX577552


title: TAX577519


title: TAX577252


title: TAX577563


title: TAX577163


title: TAX577543

description:
raw data file TAX577543_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577543_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5

value: LumA


title: Prostate tumor PCA0157 miRNA

description: microRNA expression profiling


title: TAX577371

value: Basal-complex


title: Prostate tumor PCA0156 miRNA

description: microRNA expression profiling


title: TAX577332


title: TAX577324


title: Prostate tumor PCA0151 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0149 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0147 miRNA

description: microRNA expression profiling


title: TAX577018


title: TAX577148


title: Prostate tumor PCA0146 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0155 miRNA

description: microRNA expression profiling


title: TAX577443


title: Prostate tumor PCA0144 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0145 miRNA

description: microRNA expression profiling


title: TAX577432


title: TAX577158


title: Prostate tumor PCA0141 miRNA

description: microRNA expression profiling


title: TAX577413


title: Prostate tumor PCA0136 miRNA

description: microRNA expression profiling


title: TAX577265


title: TAX577277


title: TAX577403


title: Prostate tumor PCA0134 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0132 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0135 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0130 miRNA

description: microRNA expression profiling


title: TAX577423


title: Prostate tumor PCA0129 miRNA

description: microRNA expression profiling


title: TAX577134


title: Prostate tumor PCA0128 miRNA

description: microRNA expression profiling


title: TAX577228


title: TAX577406


title: TAX577337


title: Prostate tumor PCA0125 miRNA

description: microRNA expression profiling


title: TAX577390

description:
raw data file TAX577390_Cy3_1.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5
raw data file TAX577390_Cy3_2.gpr is labeled as follows: ch1 = Cy3, ch2 = Cy5


title: Prostate tumor PCA0124 miRNA

description: microRNA expression profiling


title: TAX577378


title: Prostate tumor PCA0120 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0122 miRNA

description: microRNA expression profiling


title: TAX577424


title: Prostate tumor PCA0126 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0127 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0119 miRNA

description: microRNA expression profiling


title: TAX577380


title: Prostate tumor PCA0117 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0118 miRNA

description: microRNA expression profiling


title: TAX577393


title: TAX577218


title: Prostate tumor PCA0115 miRNA

description: microRNA expression profiling


title: TAX577557

value: amplifier


title: Prostate tumor PCA0114 miRNA

description: microRNA expression profiling


title: TAX577147


title: TAX577190


title: TAX577199

value: Luminal-complex


title: TAX577152


title: TAX577135


title: TAX577436


title: TAX577124


title: Prostate tumor PCA0112 miRNA

description: microRNA expression profiling

value: Prostate


title: Prostate tumor PCA0111 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0113 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0109 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0110 miRNA

description: microRNA expression profiling


title: TAX577024

value: sporadic


title: TAX577399

value: Basal


title: TAX577518


title: TAX577281


title: Prostate tumor PCA0108 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0107 miRNA

description: microRNA expression profiling


title: TAX577116


title: TAX577073

value: LumB


title: Prostate tumor PCA0105 miRNA

description: microRNA expression profiling

value: Primary tumor


title: TAX577192


title: GM4DC_LPS+IFNg_20hrs_rep2

city: Pittsburgh

first: Penelope

middle: Anne

last: Morel

state: PA

address: 200 Lothrop Street, BST E1048

department: Immunology

institute: University of Pittsburgh

description: The RNA labeling and microarray analysis was performed by the PittArray Facility

hyb_protocol: The resulting biotinylated cRNA was cleaned up using an Affymetrix RNA clean up column. An aliquot of 20 micrograms of cRNA was incubated at 94oC in fragmentation buffer for 35 minutes to break the RNA into segments of 35 to 200 bases. A 1μl aliquot of the sample was run on an Agilent Bioanalyzer to verify that fragmentation had resulted in RNA of the desired size distribution. Fifteen micrograms of the fragmented RNA was added to a final volume of 300 μl hybridization cocktail (Affymetrix). An appropriate volume of this sample was applied to the Affymetrix MG U74Av2 gene chip and the chip was incubated overnight at 45oC with rotation. Following hybridization the sample was removed and the GeneChip cassette filled with non-stringent wash buffer. The chips were loaded onto an Affymetrix Fluidics station for wash and stain.

scan_protocol: Samples were scanned using the GeneArray® scanner.

data_processing: Affymetrix MAS5 algorithm

source_name: GM + IL4 Dendritic cells exposed to LPS + IFNg

label_protocol: ENZO BioArray high efficiency RNA transcript labeling kit

growth_protocol: BM cultured for 4 days in GM-CSF (1ng/ml) + IL-4 (1ng/ml). DC purified on 14.5% metrizamide gradient.

extract_protocol: Qiagen kit

treatment_protocol: GM and GM4 DC (10^6/ml) were cultured in the presence of LPS (10 µg/ml) (Sigma) and IFN-γ (50 ng/ml) (BD PharMingen). Cells were harvested at 0, 6 and 20 hours after activation and total RNA was isolated according to Qiagen’s protocol (Qiagen Inc). Each time point was replicated 2-3 times; thus a total of 15 microarrays were used for the current analysis.

tag: gender

value: female

tag: age

value: 6-8 weeks

tag: cells

value: dendritic cells from bone marrow

tag: strain

value: NOD (non-obese diabetic)


title: Prostate tumor PCA0103 miRNA

description: microRNA expression profiling

tag: sample id

tag: disease status


title: TAX577525

value: Breast tumor

tag: reference


title: TAX577335

tag: tissue

value: promega male reference


title: GMDC_LPS+IFNg_20hrs_rep2

source_name: GM Dendritic cells exposed to LPS + IFNg

growth_protocol: BM cultured for 4 days in GM-CSF (1ng/ml). DC purified on 16% metrizamide gradient.


title: GM4DC_LPS+IFNg_6hrs_rep3


title: GMDC_LPS+IFNg_20hrs_rep1


title: GM4DC_LPS+IFNg_0hr_rep3


title: TAX577186

tag: hu subtype


title: GM4DC_LPS+IFNg_20hrs_rep1


title: Prostate tumor PCA0101 miRNA

description: microRNA expression profiling

value: prostate cancer


title: GMDC_LPS+IFNg_0hrs_rep2

source_name: GM Dendritic cells prior to LPS exposure


title: Prostate tumor PCA0104 miRNA

description: microRNA expression profiling


title: GM4DC_LPS+IFNg_6hrs_rep2


title: GMDC_LPS+IFNg_6hrs_rep2


title: Prostate tumor PCA0099 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0097 miRNA

description: microRNA expression profiling


title: TAX577362

tag: familial status

value: familial


title: Prostate tumor PCA0096 miRNA

description: microRNA expression profiling


title: GMDC_LPS+IFNg_0hrs_rep3


title: GM4DC_LPS+IFNg_0hr_rep2


title: GM4DC_LPS+IFNg_0hr_rep1

growth_protocol: BM cultured for 4 days in GM-CSF + IL-4


title: TAX577162

tag: er


title: TAX577510

value: LumA

tag: osbin

value: Luminal-simple


title: GMDC_LPS+IFNg_6hrs_rep1

treatment_protocol: GM DC (10^6/ml) were cultured in the presence of LPS (10 µg/ml) (Sigma) and IFN-γ (50 ng/ml) (BD PharMingen). Cells were harvested at 0, 6 and 20 hours after activation and total RNA was isolated according to Qiagen’s protocol (Qiagen Inc). Each time point was replicated 2-3 times; thus a total of 15 microarrays were used for the current analysis.


title: Prostate tumor PCA0095 miRNA

description: microRNA expression profiling


title: TAX577307

value: Normal

tag: os


title: GMDC_LPS+IFNg_0hrs_rep1


title: Prostate tumor PCA0094 miRNA

description: microRNA expression profiling


title: TAX577339

tag: pgr

value: Basal-complex


title: Prostate tumor PCA0093 miRNA

description: microRNA expression profiling

value: Prostate

tag: tumor type


title: GM4DC_LPS+IFNg_6hr_rep1


title: TAX577370

tag: grade


title: TAX577412

tag: genomic subtype


title: Prostate tumor PCA0092 miRNA

description: microRNA expression profiling


title: stac embryos 30hpf, biological rep1

city: Beijing

first: Xinyi

last: Zhao

address: Haidian District, Tsinghuayuan, No.1

department: Department of Biological Sciences and Biotechnology

institute: Tsinghua University

description: Gene expression data from mutant (stac) embryos

hyb_protocol: Following fragmentation,1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Zebrafish Genome Array with Hybridization Oven 640: Affymetrix, 800139 (220V). GeneChips were washed and stained in the Fluidics Station 450: Affymetrix, P/N 00-0079

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000: Affymetrix, P/N 00-00212

data_processing: The data were analyzed with Microarray Suite 5.0

organism: Danio rerio

source_name: Denio rerio embryos at 30hpf

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8ug total RNA, and labeling was carried out at 37C for 16hr. Biotinylated cRNA was purifed by QIAGEN RNeasy Total RNA Isolation kit.

growth_protocol: Embryos were obtained from crossing of stac heterozygous and classified by phenotype and EGFP expression. These embryos were raised in holfreter water and collected at 24hpf and 30hpf.

extract_protocol: Total RNA was isolated with Rneasy@ Mini Kit according to the protocol "Purification of total RNA from animal tissues" on Rneasy@ Mini Handbook (Quagen).

treatment_protocol: Embryo were dechorionated with proteinase K and homogenized by Buffer RLT (Rneasy@ Mini Kit, Qiagen).

tag: treatment

value: embryo dechorionation

tag: genotype/variation

value: stac mutant


title: TAX577119


title: wild type embryos 30hpf, biological rep2

description: Gene expression data from wild type embryos

value: wild type

tag: age


title: wild type embryos 24hpf, biological rep2

source_name: Denio rerio embryos at 24hpf


title: wild type embryos 24hpf, biological rep1


title: wild type embryos 30hpf, biological rep1


title: TAX577553

value: sporadic

value: Luminal-complex


title: Prostate tumor PCA0090 miRNA

description: microRNA expression profiling

value: Primary tumor


title: stac embryos 24hpf, biological rep2


title: Prostate tumor PCA0089 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0087 miRNA

description: microRNA expression profiling


title: stac embryos 30hpf, biological rep2


title: stac embryos 24hpf, biological rep1


title: TAX577334

value: Basal

value: mixed


title: TAX577322

value: Breast tumor


title: TAX577222

value: promega male reference


title: TAX577429


title: Prostate tumor PCA0080 miRNA

description: microRNA expression profiling

value: prostate cancer


title: Prostate tumor PCA0081 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0086 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0082 miRNA

description: microRNA expression profiling


title: Prostate tumor PCA0077 miRNA

description: microRNA expression profiling


title: TAX577573

value: LumB


title: Prostate tumor PCA0075 miRNA

description: microRNA expression profiling