title: 38h-01_Vivo

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description:
Biological replicate 1 of 4.
raw data file: E_38H-01_CY3-300_CY5-470.gpr

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix 4200L dual-channel laser scanner

data_processing: Background correction: backgroundCorrect 'normexp', Normalization: normalizeWithinArrays 'loess', Correlation of spot duplicat: duplicateCorrelation, Adjust to linear method: lmFit, Statistical analysis: eBayes, decideTests 'global' 'BY'[statistical results provided as Series Supplementary file].

organism: Clostridioides difficile

source_name: R20291 extracted after 38h in vivo growth

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark. DNA samples were labelled using the Bioprime plus array CGH indirect genomic labeling system (invitrogen)

growth_protocol: We did a 9 hours preculture of Clostridium difficile R20291 in Tryptone yeast extract (TY), we centrifuged and resuspended in PBS. Then we gave 5ml of this preparation to 6 mouses  per time point (C. difficile monoxenic mouse model). Finally mouse were sacrificed, according European rules, at different time 4, 6, 8, 14 and 38 hours after infection to collect the luminal and mucosa associated bacteria in the caeca.

extract_protocol: Total RNA extracted using RNAPro Blue (FastPrep) and following Qbiogen manufacturer's instructions

tag: strain background

value: wild type

source_name: R20291 grown 14H in PY (reference)


title: 38h-06_Vivo

status: Public on Jan 31 2016

type: RNA

description:
Biological replicate 4 of 4.
raw data file: H_38H-06_CY3-420_CY5-370.gpr

molecule: total RNA

tag: genotype/variation


title: UM-UC-3_DMSO_24h_rep2

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

description: gene expression data from DMSO treated UM-UC-3 cells

hyb_protocol: After fragmentation labeled aRNA was hybridized to Affymetrix PrimeView Human Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturer´s protocol

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing: Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by RMA after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability . Input data pre-processing was concluded by baseline transformation to the median of all samples

label: biotin

organism: Homo sapiens

source_name: Urothelial carcinoma UM-UC-3 cells treated with 0.1% DMSO for 24 h

label_protocol: Synthesis of cDNA and subsequent biotin labeling of cRNA was performed according to the manufacturer´s protocol (3´ IVT Plus Kit; Affymetrix, Inc.). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and biotin labeling of aRNA

growth_protocol: Cells were grown in DMEM supplemented with 10 % FCS.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer´s instruction.

treatment_protocol: Cells were treated with 0.1 % DMSO, 3 nM Romidepsin, 0.5 µM Givinostat, or 2.5 M SAHA for 24 h.

tag: cell line

tag: tumor type

value: urothelial cancer


title: UM-UC-3_DMSO_24h_rep1


title: UM-UC-3_Romidepsin_24h_rep3

description: gene expression data from Romidepsin treated UM-UC-3 cells

source_name: Urothelial carcinoma UM-UC-3 cells treated with 3 nM Romidepsin for 24 h


title: colorectal carcinoma cells with defunct TP53 using TAS ChipM

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with TAS.

hyb_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

scan_protocol: Affymetrix Human Tiling 1.0 array were proceed using the GCS3000 7G system according to manufacturer's protocol.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with Tiling Array Software (TAS) using standard parameters according to Kampa et al. ("Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.". Genome Research, 14:331-42, 2004.). We set bandwith=35, i.e. on average the probe intensities are smoothed by calculating the Hodges-Lehman estimator over 3 probes, and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal length of segments to be reported as highly expressed was set to minrun=90. Perfect match (PM) and mismatch (MM) probe intensities were utilized in using an intensity threshold of 150.

source_name: Colorectal carcinoma cells with defunct TP53

label_protocol: 10µg RNA were analyzed on Affymetrix Human Tiling 1.0 array set according to the manufacturer's protocol.

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

tag: cell type

value: colorectal carcinoma cells

tag: treatment

value: with defunct TP53


title: 38h-05_Vivo

description:
Biological replicate 3 of 4.
raw data file: G_38H-05_CY3-430_CY5-370.gpr


title: 38h-02_Vivo

description:
Biological replicate 2 of 4.
raw data file: F_38H-02_CY3-300_CY5-470.gpr


title: INA6 cells using TAS (IL-6 withdrawal) ChipM

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with Tiling Array Software (TAS).

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

tag: tumor

value: multiple myeloma

value: IL-6 has been withdrawn for 13 hours


title: INA6 cells using TAS (IL-6 restimulation) ChipM

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with Tiling Array Software (TAS).

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: 8H-05_Vivo

description:
Biological replicate 3 of 4.
raw data file: C_8h-05_cy3-420_cy5-370.gpr

source_name: R20291 extracted after 8h in vivo growth


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipM

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with MAT.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.). Parameters for MAT as given in Johnson et al. are geared towards ChIP-chip analysis and, thus, not suitable for expression analysis. Upon inspection of positive control transcripts, we identified optimal parameters for MAT as the same or analogous values as taken for TAS (Tiling Array Software). We set bandwith=35 and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal probe count was set to minprobe=3. Only perfect match (PM) probe intensities were utilized. A p-value threshold for expression analyses was set to 1e-5 which yielded the best results from the set of tested parameter values.

source_name: Colorectal carcinoma cells with overexpressed TP53

value: induced expression of TP53


title: 8H-01_Vivo

description:
Biological replicate 1 of 4.
raw data file: A_8h-01_cy3-300_cy5-470.gpr


title: 8H-06_Vivo

description:
Biological replicate 4 of 4.
raw data file: D_8h-06_cy3-430_cy5-370.gpr


title: UM-UC-3_Romidepsin_24h_rep1


title: 6h-06_Vivo

description:
Biological replicate 4 of 4.
raw data file: H_6h-06_cy3-310_cy5-470.gpr

source_name: R20291 extracted after 6h in vivo growth


title: 8H-02_Vivo

description:
Biological replicate 2 of 4.
raw data file: B_8H-02_CY3-300_CY5-470.gpr


title: 6h-05_Vivo

description:
Biological replicate 3 of 4.
raw data file: G_6h-05_cy3-310_cy5-470.gpr


title: colorectal carcinoma cells with defunct TP53 using MAT ChipM

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with MAT.

value: defunct TP53


title: UM-UC-3_DMSO_24h_rep3


title: UM-UC-3_Romidepsin_24h_rep2


title: INA6 cells using MAT (IL-6 withdrawal) ChipM

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with MAT.


title: INA6 cells using MAT (IL-6 restimulation) ChipM

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with MAT.


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipF

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with our novel permutation algorithm TileShuffle.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. The expression data were processed with our new permutation approach TileShuffle. TileShuffle was applied using only perfect match (PM) probes, a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, three GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).


title: Patient 84 CRT Responder

city: Boston

first: Saumya

last: Das

state: MA

address: CLS907 330 Brookline Ave

department: Cardiology

country: USA

institute: Beth Israel Deaconess Medical Center

data_processing: Global normalization, p values adjusted with Benjamini-Hochberg correction for 5% FDR

label: FAM

source_name: peripheral serum at time of CRT implant

label_protocol: the signals were generated using qRT PCR on an ABI low-density array, using FAM as the fluorophore. there was no separate labeling step

extract_protocol: miRVANA micro RNA isolation kit, life technologies Cat No AM1560

tag: condition

value: LBBB, non-ischemic myopathy, >10%change in EF at six months

tag: gender

value: male


title: 6h-02_Vivo

description:
Biological replicate 1 of 4.
raw data file: E_6h-02_cy3-440_cy5-390.gpr


title: Patient 83 CRT Responder


title: Patient 78 CRT Non-responder

value: LBBB, non-ischemic myopathy, <10%change in EF at six months


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipF

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with our permutation approach (TileShuffle).


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipF

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with our permutation approach (TileShuffle).


title: 4H-06_Vivo

description:
Biological replicate 4 of 4.
raw data file: D_4h-06_cy3-300_cy5-470.gpr

source_name: R20291 extracted after 4h in vivo growth


title: Patient 70 CRT Non-responder


title: UM-UC-3_DMSO_24h_rep1

description: gene expression data from DMSO treated UM-UC-3 cells


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipF

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with TAS.


title: 4H-05_Vivo

description:
Biological replicate 3 of 4.
raw data file: C_4h-05_cy3-310_cy5-470.gpr


title: VM-CUB1_SAHA_24h_rep1

description: gene expression data from SAHA treated VM-CUB1 cells

source_name: Urothelial carcinoma VM-CUB1 cells treated with 2.5 µM SAHA for 24 h


title: colorectal carcinoma cells with defunct TP53 using TAS ChipF

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with TAS.


title: VM-CUB1_DMSO_24h_rep3

description: gene expression data from DMSO treated VM-CUB1 cells

source_name: Urothelial carcinoma VM-CUB1 cells treated with 0.1% DMSO for 24 h


title: Patient 66 CRT Non-responder


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipF

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with our novel permutation approach TileShuffle.


title: VM-CUB1_DMSO_24h_rep2


title: INA6 cells using TAS (IL-6 withdrawal) ChipF

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with Tiling Array Software (TAS).


title: 4H-04_Vivo

description:
Biological replicate 2 of 4.
raw data file: B_4h-04_cy3-420_cy5-390.gpr


title: INA6 cells using TAS (IL-6 restimulation) ChipF

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with Tiling Array Software (TAS).


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipF

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with MAT.


title: Patient 40 CRT Non-responder


title: 6h-04_Vivo

description:
Biological replicate 2 of 4.
raw data file: F_6h-04_cy3-450_cy5-380.gpr


title: VM-CUB1_SAHA_24h_rep2


title: VM-CUB1_Givinostat_24h_rep3

description: gene expression data from Givinostat treated VM-CUB1 cells

source_name: Urothelial carcinoma VM-CUB1 cells treated with 0.5 µM Givinostat for 24 h


title: Patient 24 CRT Non-responder


title: 4H-02_Vivo

description:
Biological replicate 1 of 4.
raw data file: A_4h-02_cy3-420_cy5-390.gpr


title: colorectal carcinoma cells with defunct TP53 using MAT ChipF

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with MAT.


title: VM-CUB1_DMSO_24h_rep1


title: Patient 14 CRT Non-responder


title: VM-CUB1_SAHA_24h_rep3


title: INA6 cells using MAT (IL-6 withdrawal) ChipF

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with MAT.


title: Patient 115 CRT Responder


title: VM-CUB1_Givinostat_24h_rep2


title: Patient 59 CRT Responder


title: VM-CUB1_Romidepsin_24h_rep3

description: gene expression data from Romidepsin treated VM-CUB1 cells

source_name: Urothelial carcinoma VM-CUB1 cells treated with 3 nM Romidepsin for 24 h


title: INA6 cells using MAT (IL-6 restimulation) ChipF

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with MAT.


title: Patient 109 CRT Responder


title: VM-CUB1_DMSO_24h_rep2


title: VM-CUB1_Romidepsin_24h_rep1


title: VM-CUB1_Givinostat_24h_rep1


title: VM-CUB1_Romidepsin_24h_rep2


title: Complicated malaria 14 (PFC-23)

status: Public on Jan 30 2016

city: Pilani

first: Ashis

middle: Kumar

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

country: India

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

description:
PFC-23
Gene expression of parasite isolates.

hyb_protocol: The labeled cRNA samples were hybridized on to a custom P. falciparum 8x15k Array (AMADID: 024956) designed by Genotypic Technology Pvt. Ltd., Bangalore, India. 600ng of Cy3-labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanning was performed using the Agilent Microarray Scanner (Agilent, Palo Alto, CA, G Model G2565BA) at 5 micron resolution.

data_processing: Data extraction from images was done using Feature Extraction software (Agilent Technologies). Feature extracted data was analyzed using GeneSpring GX Version 11.5 software from Agilent. All the probes were normalized using quantile-based normalization method. After normalization, only probes detected in at least 30% of samples were considered for further analysis to create weighted gene co-expression-based systems network.

organism: Plasmodium falciparum

source_name: P. falciparum parasites from patient's blood, complicated malaria

label_protocol: Parasite total RNA samples for gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the samples were incubated with reverse transcription mix at 40°C and converted to double-stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned-up double-stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP (Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C.

growth_protocol: P. falciparum isolates were collected directly from infected patients with differing clinical symptoms.

extract_protocol: Total RNA was extracted using TriReagent (Sigma Aldrich, USA) following manufacturer's instructions.

treatment_protocol: Blood was immediately (within 15 minutes of collection) subjected to density gradient-based separation (Histopaque 1077, Sigma Aldrich, USA) to separate the peripheral blood mononuclear cells (PBMCs) from the infected and uninfected erythrocytes following manufacturer’s instructions. Both fractions were washed with phosphate-buffered saline (PBS) twice and lysed using 4 volume of Tri-Reagent (Sigma Aldrich, USA) and stored at -80°C.

value: P. falciparum parasites

tag: patient's age (yr)

tag: patient's gender

value: M

tag: patient's clinical presentation

value: jaundice


title: VM-CUB1_DMSO_24h_rep3


title: Complicated malaria 11 (PFC-19)

description:
PFC-19
Gene expression of parasite isolates.

value: renal failure


title: Complicated malaria 12 (PFC-21)

description:
PFC-21
Gene expression of parasite isolates.

value: renal failure, thrombocytopenia


title: Complicated malaria 7 (PFC-14)

description:
PFC-14
Gene expression of parasite isolates.

value: cerebral malaria, jaundice, thrombocytopenia


title: Complicated malaria 1 (PFC-03)

description:
PFC-03
Gene expression of parasite isolates.

value: jaundice, renal failure, thrombocytopenia


title: Complicated malaria 15 (PFC-25)

description:
PFC-25
Gene expression of parasite isolates.

value: jaundice, thrombocytopenia


title: Complicated malaria 13 (PFC-22)

description:
PFC-22
Gene expression of parasite isolates.


title: Complicated malaria 5 (PFC-11)

description:
PFC-11
Gene expression of parasite isolates.

value: F

value: jaundice, anemia


title: Uncomplicated malaria 6 (PFU-06)

description:
PFU-06
Gene expression of parasite isolates.

source_name: P. falciparum parasites from patient's blood, uncomplicated malaria

value: uncomplicated malaria


title: Uncomplicated malaria 7 (PFU-07)

description:
PFU-07
Gene expression of parasite isolates.


title: Uncomplicated malaria 5 (PFU-05)

description:
PFU-05
Gene expression of parasite isolates.


title: Complicated malaria 16 (PFC-29)

description:
PFC-29
Gene expression of parasite isolates.

value: cerebral malaria, anemia


title: Complicated malaria 3 (PFC-06)

description:
PFC-06
Gene expression of parasite isolates.


title: Complicated malaria 2 (PFC-05)

description:
PFC-05
Gene expression of parasite isolates.


title: Complicated malaria 4 (PFC-10)

description:
PFC-10
Gene expression of parasite isolates.


title: Complicated malaria 6 (PFC-12)

description:
PFC-12
Gene expression of parasite isolates.


title: VM-CUB1_DMSO_24h_rep1

description: gene expression data from DMSO treated VM-CUB1 cells

value: urothelial cancer


title: Complicated malaria 10 (PFC-18)

description:
PFC-18
Gene expression of parasite isolates.


title: Complicated malaria 8 (PFC-15)

description:
PFC-15
Gene expression of parasite isolates.


title: Uncomplicated malaria 3 (PFU-03)

description:
PFU-03
Gene expression of parasite isolates.


title: Complicated malaria 9 (PFC-17)

description:
PFC-17
Gene expression of parasite isolates.

value: jaundice, renal failure


title: Uncomplicated malaria 4 (PFU-04)

description:
PFU-04
Gene expression of parasite isolates.


title: Shiozawa_016_038

city: Winston-Salem

first: Yusuke

last: Shiozawa

state: NC

address: 1 Medical Center Blvd

department: Cancer Biology

institute: Wake Forest School of Medicine

hyb_protocol: Following Labeling procedure, 2.5 ug of cDNA were hybridized at 48C on Human Gene ST 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515).

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515)

data_processing: Data was analyzed using the oligo Bioconductor packages implemented in the R-statistical environment version 3.0.0. RMA was used to fit log2 transformed expression values

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 25 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 2.5 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6)

growth_protocol: Prostate cancer cells (PC3, C4-2B, 1,000,000 cells/100ul of growth medium) were innoculated into SCID mice by intracadiac injection.

extract_protocol: The extractions and purifications of RNA from the resulting cells were performed using RNeasy Plus Micro RNA kit, which allowed RNA isolation and DNAse treatment from small cell numbers. RNA samples were submitted to the University of Michigan Sequencing core for quality evaluation followed by microarray analysis using an Affymetrix platform.

treatment_protocol: At 24 h later, the CD133+/CD44+ fraction and CD133-/CD44- fraction were sorted with a FACSAria II Cell Sorter from in vitro cultured prostate cancer cells (PC3, C4-2B) and in vivo disseminated prostate cancer cells (PC3, C4-2B) obtained from bone marrow of SCID mice innoculated with prostate cancer cells.

value: prostate cancer

tag: cell population

tag: cell source

value: in vivo


title: Shiozawa_009_031

source_name: PC3, CD133-/CD44-, in vivo


title: Shiozawa_013_035


title: Shiozawa_006_012

source_name: PC3, CD133+/CD44+, in vitro

value: in vitro


title: MCF7_control siRNA_6 hr_vehicle rep2

city: Dunedin

first: Julia

last: Horsfield

state: Otago

address: Corner of Great King and Hannover Streets

department: Pathology

country: New Zealand

institute: University of Otago

description:
JH0006
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA for 48 hrs and then treated with vehicle for 6 hours

hyb_protocol: Standard AffymetrixProtocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3.2001) using Affymetrix GeneChip Hybridisation oven 640

scan_protocol: Standard AffymetrixProtocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3.2001) using Affymetrix GeneChip Scanner 7G

data_processing: Data was pre-pocessed and normalized using RMA. A number of plots were used to visualise the normalised data in order to analyse the adequacy of data transformation.

source_name: MCF7_control siRNA_6 hr veh

label_protocol: RNAs from 3 independent experiments were labelled and hybridised to Affymetrix PrimeView Human Gene Expression arrays using 3' IVT Express kit according to manufacturer’s instructions

growth_protocol: MCF7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) media (Life technologies or Sigma) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated using the Machery Nagel Nucleospin RNA Isolation kit according to manufacturer’s guidelines (Machery Nagel).

treatment_protocol: For hormone depletion, MCF7 cells were cultured for 3 days in phenol-red free DMEM media supplemented with 10% charcoal dextran (Sigma) treated FBS.  Hormone depleted cells were treated with 17-β estradiol (Sigma) at a final concentration of 100 nM for various time periods. Estradiol was dissolved in absolute ethanol, and as, controls hormone depleted cells were also treated with the same volume of ethanol (vehicle) for the same time periods.

value: estrogen receptor positive breast cancer cells

tag: transfected with

value: control siRNA

tag: treated with

value: vehicle for 6hrs


title: MCF7_RAD21 siRNA_6 hr_Estrogen rep2

description:
JH0007
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs and then treated with estrogen for 6 hours

source_name: MCF7_RAD21 siRNA_6 hr estrogen

value: RAD21 siRNA

value: 100 nM 17-β estradiol for 6hrs


title: Shiozawa_011_033


title: Shiozawa_004_010


title: Shiozawa_005_011

source_name: PC3, CD133-/CD44-, in vitro


title: MCF7_RAD21 siRNA_6 hr_Estrogen rep1

description:
JH0003
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs and then treated with estrogen for 6 hours


title: MCF7_control siRNA_6 hr_Estrogen rep1

description:
JH0001
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA for 48 hrs and then treated with estrogen for 6 hours

source_name: MCF7_control siRNA_6 hr estrogen


title: MCF7_RAD21 siRNA_6 hr_vehicle rep3

description:
JH0012
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs and treated with vehicle for 6 hours

source_name: MCF7_RAD21 siRNA_6 hr veh


title: MCF7_RAD21 siRNA_6 hr_vehicle rep2

description:
JH0008
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs and treated with vehicle for 6 hours


title: MCF7_RAD21 siRNA_6 hr_Estrogen rep3

description:
JH0011
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs and then treated with estrogen for 6 hours


title: Shiozawa_003_009


title: Shiozawa_002_002

source_name: C4-2B, CD133+/CD44+, in vitro


title: MCF7_RAD21 siRNA_6 hr_vehicle rep1

description:
JH0004
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs and treated with vehicle for 6 hours


title: Shiozawa_014_036

source_name: C4-2B, CD133-/CD44-, in vitro


title: Shiozawa_007_029


title: Shiozawa_015_037


title: Shiozawa_010_032


title: Shiozawa_001_001


title: Shiozawa_012_034

source_name: PC3, CD133+/CD44+, in vivo


title: MCF7_control siRNA_6 hr_Estrogen rep3

description:
JH0009
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA for 48 hrs and then treated with estrogen for 6 hours


title: PLEXdb_VV35_S12

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description:
genotype: Wild type Ugni Blanc - developmental stage name: 8 DAA fruit - rep3
Berries were harvested 8 days after anthesis on the wild type Ugni Blanc (May still include original submitter created erros/discrepancies)

hyb_protocol: CNB Grapegen Affymetrix hybridization

scan_protocol: CNB Grapegen Affymetrix scanning

data_processing: RMA normalization was performed for Affymetrix Platforms: Using APT (apt-1.12.0: apt-probeset-summarize.cpp,v 1.178).

organism: Vitis vinifera

source_name: fruit (genotype: Wild type Ugni Blanc - developmental stage name: 8 DAA fruit)

label_protocol: CNB Grapegen Affymetrix labeling

extract_protocol: Spectrum +RNeasy

tag: germplasm name

tag: organism part

tag: development stage

value: fruit development stages ('PO:0001002')

tag: growth media

value: field soil


title: MCF7_control siRNA_6 hr_vehicle rep1

description:
JH0002
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA for 48 hrs and then treated with vehicle for 6 hours

tag: cell line


title: Shiozawa_008_030

tag: cell type


title: MCF7_control siRNA_6 hr_Estrogen rep2

description:
JH0005
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA for 48 hrs and then treated with estrogen for 6 hours


title: MCF7_control siRNA_6 hr_vehicle rep3

description:
JH0010
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA for 48 hrs and then treated with vehicle for 6 hours


title: Patient 69 CRT Responder

source_name: peripheral serum at time of CRT implant

value: LBBB, non-ischemic myopathy, >10%change in EF at six months

value: male


title: PLEXdb_VV35_S11

description:
genotype: Wild type Ugni Blanc - developmental stage name: 8 DAA fruit - rep2
Berries were harvested 8 days after anthesis on the wild type Ugni Blanc (May still include original submitter created erros/discrepancies)


title: MCF7_RAD21 siRNA_3 hr_Estrogen rep1

description:
TD0003
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs and then treated with estrogen for 3 hours

source_name: MCF7_RAD21 siRNA_3 hr estrogen

value: 100 nM 17-β estradiol for 3hrs


title: PLEXdb_VV35_S9

description:
genotype: Wild type Ugni Blanc - developmental stage name: Flower - rep3
Flowers at stage 18E-L were harvested on the wild type Ugni Blanc (May still include original submitter created erros/discrepancies)

source_name: flower (genotype: Wild type Ugni Blanc - developmental stage name: Flower)


title: MCF7_RAD21 siRNA_3 hr_Estrogen rep2

description:
TD0007
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs and then treated with estrogen for 3 hours


title: PLEXdb_VV35_S8

description:
genotype: Wild type Ugni Blanc - developmental stage name: Flower - rep2
Flowers at stage 18E-L were harvested on the wild type Ugni Blanc (May still include original submitter created erros/discrepancies)


title: PLEXdb_VV35_S10

description:
genotype: Wild type Ugni Blanc - developmental stage name: 8 DAA fruit - rep1
Berries were harvested 8 days after anthesis on the wild type Ugni Blanc (May still include original submitter created erros/discrepancies)


title: MCF7_control siRNA_3 hr_Estrogen rep3

description:
TD0009
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA and then treated with estrogen for 3 hours

source_name: MCF7_control siRNA_3 hr estrogen


title: MCF7_RAD21 siRNA_3 hr_Estrogen rep3

description:
TD0011
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs and then treated with estrogen for 3 hours


title: PLEXdb_VV35_S4

description:
genotype: flb somatic variant - developmental stage name: 8 DAA fruit - rep1
Berries were harvested 8 days after anthesis on the flb somatic variant (May still include original submitter created erros/discrepancies)

source_name: fruit (genotype: flb somatic variant - developmental stage name: 8 DAA fruit)


title: MCF7_control siRNA_3 hr_vehicle rep3

description:
TD0010
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA for 48 hrs and then treated with vehicle for 3 hours

source_name: MCF7_control siRNA_3 hr veh

value: vehicle for 3hrs


title: MCF7_control siRNA_3 hr_Estrogen rep2

description:
TD0005
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA and then treated with estrogen for 3 hours


title: MCF7_RAD21 siRNA_3 hr_vehicle rep2

description:
TD0008
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs  and then treated with vehicle for 3 hours

source_name: MCF7_RAD21 siRNA_3 hr veh


title: HEK293T PUM1+2 siRNA pool rep_3 48h

city: Ankara

first: Saber

last: HafezQorani

state: Ankara

address: Bioinformatics Lab, Informatics Institute, Middle East Technical University, Üniversiteler Mah. Dumlupınar Blv. No:1, 06800 Çankaya Ankara/TURKEY

department: Health Informatics

country: Turkey

institute: Middle East Technical University

description:
Total cell lysate RNA.
Knockdown replicate 3.
3998355016_G
SAMPLE 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using the iScan system (Illumina, Inc.), and the fluorescence intensities were analyzed and annotated using GenomeStudio software (Illumina, Inc.)

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

label: Biotin

source_name: HEK293T, PUM1+2 siRNA, 48h

label_protocol: Standard labeling protocol.

growth_protocol: HEK293T cells were maintained at 37⁰C at 5% CO2 in Dulbecco's Modified Eagle's Medium (DMEM), high glucose (4500mg/L), supplemented with Penicillin (100units/ml), Streptomycin (100μg/ml), Glutamine (2mM) and 10% heat-inactivated fetal calf serum.

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

treatment_protocol: siRNA pools for Pumilio 1 and Pumilio 2 (siRNAs from Dharmacon/GE) were mixed and diluted to a final concentration of 50nM and transfected overnight in a 24-wells culture plate.

tag: sirna

value: PUM1+2 siRNA pool


title: HEK293T PUM1+2 siRNA pool rep_1 48h

description:
Total cell lysate RNA.
Knockdown replicate 1.
3998355016_J
SAMPLE 1


title: HEK293T PUM1+2 siRNA pool rep_4 48h

description:
Total cell lysate RNA.
Knockdown replicate 4.
3998355016_H
SAMPLE 4


title: HEK293T non-targeting siRNA pool rep_3 48h

description:
Total cell lysate RNA.
Control replicate 3.
3998355016_L
SAMPLE 7

source_name: HEK293T, control siRNA, 48h

value: non-targeting siRNA pool


title: HEK293T non-targeting siRNA pool rep_2 48h

description:
Total cell lysate RNA.
Control replicate 2.
3998355016_K
SAMPLE 6


title: HEK293T PUM1+2 siRNA pool rep_2 48h

description:
Total cell lysate RNA.
Knockdown replicate 2.
3998355016_I
SAMPLE 2


title: MCF7_RAD21 siRNA_3 hr_vehicle rep3

description:
TD0012
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs  and then treated with vehicle for 3 hours


title: HEK293T non-targeting siRNA pool rep_1 48h

description:
Total cell lysate RNA.
Control replicate 1.
3998355016_F
SAMPLE 5


title: PLEXdb_VV35_S3

description:
genotype: flb somatic variant - developmental stage name: Flower - rep3
Flowers at stage 18E-L were harvested on the flb somatic variant (May still include original submitter created erros/discrepancies)

source_name: flower (genotype: flb somatic variant - developmental stage name: Flower)


title: PLEXdb_VV35_S5

description:
genotype: flb somatic variant - developmental stage name: 8 DAA fruit - rep2
Berries were harvested 8 days after anthesis on the flb somatic variant (May still include original submitter created erros/discrepancies)


title: MCF7_control siRNA_3 hr_vehicle rep1

description:
TD0002
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA for 48 hrs and then treated with vehicle for 3 hours


title: MCF7_control siRNA_3 hr_Estrogen rep1

description:
TD0001
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA and then treated with estrogen for 3 hours


title: PLEXdb_VV35_S2

description:
genotype: flb somatic variant - developmental stage name: Flower - rep2
Flowers at stage 18E-L were harvested on the flb somatic variant (May still include original submitter created erros/discrepancies)


title: PLEXdb_VV35_S6

description:
genotype: flb somatic variant - developmental stage name: 8 DAA fruit - rep3
Berries were harvested 8 days after anthesis on the flb somatic variant (May still include original submitter created erros/discrepancies)


title: MCF7_control siRNA_3 hr_vehicle rep2

description:
TD0006
Gene expression data from hormone deprived MCF7 cells transfected with control siRNA for 48 hrs and then treated with vehicle for 3 hours


title: MCF7_RAD21 siRNA_3 hr_vehicle rep1

description:
TD0004
Gene expression data from hormone deprived MCF7 cells transfected with RAD21 siRNA for 48 hrs  and then treated with vehicle for 3 hours


title: Blood5 Treg

status: Public on Jan 29 2016

city: Melbourne

first: Jane

last: Li

state: Victoria

address: The Peter Doherty Institute of Infection and Immunity

department: Department of Microbiology and Immunology

country: Australia

institute: The University of Melbourne

description: replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Data processed with RUVinv in R using ruv package
RUVinv_Results: RUVinv generated logFC, raw p-values and multiple-testing adjusted p-values for indicated pairwise comparisons

source_name: Human peripheral blood

label_protocol: Encore Biotin module

extract_protocol: Qiagen RNEasy Micro kit

tag: surface markers

value: CD4+ CD25+ CD127lo CLA+

value: female


title: Blood5 CD8

description: replicate 5

value: CD8+ CLA+ CD45RO+


title: Blood5 CD4

description: replicate 5

value: CD4+ CD127hi CLA+ CD45RO+


title: HEK293T non-targeting siRNA pool rep_4 48h

description:
Total cell lysate RNA.
Control replicate 4.
3998355016_E
SAMPLE 8


title: PLEXdb_VV35_S1

description:
genotype: flb somatic variant - developmental stage name: Flower - rep1
Flowers at stage 18E-L were harvested on the flb somatic variant (May still include original submitter created erros/discrepancies)


title: Blood4 CD8

description: replicate 4


title: Blood3 CD8

description: replicate 3


title: Blood4 CD4

description: replicate 4


title: Blood4 Treg

description: replicate 4


title: PLEXdb_VV35_S7

description:
genotype: Wild type Ugni Blanc - developmental stage name: Flower - rep1
Flowers at stage 18E-L were harvested on the wild type Ugni Blanc (May still include original submitter created erros/discrepancies)


title: Blood3 Treg

description: replicate 3


title: F_SP8

city: LA

first: Sarah

last: Ahadome

state: CA

address: 100 Stein Plaza

department: Jules Stein

institute: UCLA

description: Fibroblasts from inflamed pemphigoig conjunctiva

data_processing: Probe-level raw data was generated with GenomeStudio. It was then loaded in R and normalized using the package 'lumi'. The 'detection' function from 'lumi' was used in order to obtain the detection p-value.

source_name: Primary explanted conjunctival fibroblasts

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

extract_protocol: RNA was extracted using Qiagen RNA extraction kit according to manufacturer's instructions. Quality control was performed with Agilent Bioanalyser at Illumina.

tag: tissue

value: Conjunctiva

tag: dif

tag: disease state


title: SU4

description: Uninflamed pemphigoid

source_name: Conjunctival whole tissue

value: DIF positive

value: Uninflamed pemphigoid


title: C18

description: Control

value: Control


title: Blood3 CD4

description: replicate 3

tag: gender


title: UM2

description: Uninflamed pemphigoid


title: Blood2 Treg

description: replicate 2


title: C23_2

description: Control


title: Blood2 CD4

description: replicate 2


title: F_SP5

value: Fibroblasts from inflamed pemphigoig conjunctiva


title: C21

description: Control


title: C20

description: Control


title: M10

description: Inflamed pemphigoid

value: Inflamed pemphigoid


title: Blood2 CD8

description: replicate 2


title: C22

description: Control


title: UM4

description: Uninflamed pemphigoig

value: Uninflamed pemphigoig


title: UM8

description: Uninflamed pemphigoid


title: UM3

description: Uninflamed pemphigoig


title: UM9

description: Uninflamed pemphigoig


title: C23

description: Control


title: M14

description: Inflamed pemphigoid


title: F_SC4

description: Fibroblasts from control conjunctiva

value: Fibroblasts from control conjunctiva


title: M1

description: Inflamed pemphigoid


title: M6

description: Inflamed pemphigoid


title: F_SC6

description: Fibroblasts from control conjunctiva


title: M12

description: Inflamed pemphigoid


title: F_SU6

description: Fibroblasts from uninflamed pemphigoid conjunctiva


title: F_SU8

value: Fibroblasts from uninflamed pemphigoid conjunctiva


title: M9

description: Inflamed pemphigoid


title: SkinE CD4

description: replicate 5

source_name: Human skin

value: CLA+ CD4+ CD127hi


title: Blood1 Treg

description: replicate 1


title: SkinD Treg

description: replicate 4

value: CLA+ CD4+ CD25+ CD127lo


title: SkinD CD4

description: replicate 4


title: SkinE CD8

description: replicate 5

value: CLA+ CD8+ CD103-


title: SkinD CD8

description: replicate 4


title: SkinC CD8

description: replicate 3


title: SkinC CD4

description: replicate 3


title: SkinC Treg

description: replicate 3


title: SkinB CD8

description: replicate 2


title: SkinA CD8

description: replicate 1


title: SkinB CD4

description: replicate 2


title: SkinA Treg

description: replicate 1


title: SkinB Treg

description: replicate 2


title: Blood1 CD4

description: replicate 1


title: SkinE Treg

description: replicate 5


title: SkinA CD4

description: replicate 1


title: HeLa FAF1 KD 1

city: Seoul

first: Soonhwa

last: SONG

address: Ewha Womans University-gil 52

department: College of Pharmacy

country: South Korea

institute: Ewha Womans Univiersity

description: replicate 1

hyb_protocol: Follwing fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provieded by the manufacturer

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions

data_processing:
The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Probes signal value was transformed by logarithm and normalized by quantile method.
Statistical significance of the expression data was determined using LPE test and Fold change in which the null hypothesis was that no difference exists among 2 groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: HeLa cell

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using Illumina TotalPrep RNA Amplification kit

growth_protocol: Cell line: HeLa  Cell type: Human cervical epithelial cell line

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Tehocnologies), purified using RNeasy columns (Qiagen) according to the manufacturers’ protocol.

treatment_protocol: HeLa cells were purchased from ATCC and cultured in EMEM supplemented with 10% fetal bovine serum, 100 units/mL of penicillin G and 100 g/mM streptomycin at 37°C in a 5% CO2-containing humidified incubator.

value: FAF1 siRNA

value: HeLa


title: YA-ES-3 stromal breast tumor from young Premenopausal

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

hyb_protocol: Agilent Technologies' manufacture procedures

scan_protocol: Slides were scanned with the Agilent Bundle Microarray Scanner System (Agilent Technologies) and data were processed using the Feature Extraction 10.7.3.1 software (Agilent Technologies).

data_processing: For analysis of replicate spots, the average intensity after background correction was calculated, normalization was performed using locally weighted linear regression (LOWESS) with α=0.2 within slides using the R software version  2.11.1 (R Development Core Team, 2010).

source_name: stromal breast tumor from young patients

growth_protocol: frozen tissue

extract_protocol: RNA concentration was determined by spectrophotometry (Nanodrop, Thermo Scientific, US), and integrity was accessed using the 2100 Bioanalyzer (Agilent Technologies,Waldbronn, Germany).

tag: age

tag: Sex

value: female

source_name: Reference

tag: sample type

value: pooled RNA


title: YA-BC-14 breast tumor from young adults Premenopausal

source_name: breast tumor from young adults patients

label_protocol: Agilent Technologies' manufacture procedures


title: YA-BC-9 breast tumor from young adults Premenopausal


title: MA-BC-5 breast tumor from middle aged Posmenopausal

source_name: breast tumor from middle aged patients


title: HeLa CTL KD 2

description: replicate 2

value: control siRNA


title: YA-BC-8 breast tumor from young adults Premenopausal


title: HeLa FAF1 KD 2

description: replicate 2


title: MA-BC-8 breast tumor from middle aged Posmenopausal


title: MA-BC-11 breast tumor from middle aged Posmenopausal


title: MA-BC-2 breast tumor from middle aged Posmenopausal


title: MA-BC-10 breast tumor from middle aged Posmenopausal


title: HeLa FAF1 KD 3

description: replicate 3


title: HeLa CTL KD 1

description: replicate 1


title: YA-ES-4 stromal breast tumor from young Premenopausal


title: YA-ES-2 stromal breast tumor from young Premenopausal


title: MA-BC-7 breast tumor from middle aged Posmenopausal


title: YA-BC-7 breast tumor from young adults Premenopausal


title: MA-BC-4 breast tumor from middle aged Posmenopausal


title: MA-ES-1 stromal breast tumor from MA Posmenopausal

source_name: stromal breast tumor from MA patients


title: YA-BC-10 breast tumor from young adults Premenopausal


title: HeLa CTL KD 3

description: replicate 3


title: YA-BC-15 breast tumor from young adults Premenopausal


title: MA-BC-13 breast tumor from middle aged Posmenopausal


title: MA-BC-6 breast tumor from middle aged Posmenopausal


title: MA-ES-5 stromal breast tumor from MA Posmenopausal


title: YA-ES-1 stromal breast tumor from young Premenopausal


title: MA-BC-12 breast tumor from middle aged Posmenopausal


title: YA-BC-6 breast tumor from young adults Premenopausal


title: MA-BC-9 breast tumor from middle aged Posmenopausal


title: MA-BC-3 breast tumor from middle aged Posmenopausal


title: YA-BC-1 breast tumor from young adults Premenopausal


title: YA-BC-13 breast tumor from young adults Premenopausal


title: MA-BC-1 breast tumor from middle aged Posmenopausal


title: YA-BC-4 breast tumor from young adults Premenopausal


title: YA-BC-5 breast tumor from young adults Premenopausal


title: YA-ES-6 stromal breast tumor from young Premenopausal


title: PB1 shoot sample grown in Phosphorus deficient conditions biological rep. 1

city: New Delhi

first: JITENDER

last: GIRI

state: Delhi

address: Aruna Asaf Ali Marg

institute: NIPGR

description:
Gene expression data of 15 days old PB1 shoot tissue raised under Phosphporus deficient condition
PB1 Shoot -P_1.CEL

hyb_protocol: Following fragmentation, 12.5 µg of cRNA were hybridized for 16 hr at 450C on Affymetrix  GeneChip®  rice genome array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: First-order analysis was performed using Affymetrix® GeneChip® Command Console® Software (AGCC). Normalization of data and differential expression analysis was done using ‘GeneSpring’ software 12.5 (Agilent Technologies Inc.)

organism: Oryza sativa

source_name: 15-day-old whole seedling of PB1 stressed

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA

growth_protocol: Seedlings of Dular and PB1 were raised on Yoshida  medium with 320 µM Phosphorus (P sufficient) and 1 µM Phosphorus (P deficient ) condition for 15 days.

extract_protocol: Extraction of total RNA was performed using RNeasy Mini Kit (Qiagen)  according to the manufacturer's instructions.

treatment_protocol: Untreated seedlings were used for tissue

tag: variety

value: 15-days-old seedlings

tag: growth condition

value: Phosphorus deficient


title: YA-BC-11 breast tumor from young adults Premenopausal


title: PB1 shoot sample grown in Phosphorus deficient conditions biological rep. 2

description:
Gene expression data of 15 days old PB1 shoot tissue raised under Phosphporus deficient condition
PB1 Shoot -P_2.CEL


title: YA-ES-5 stromal breast tumor from young Premenopausal


title: YA-ES-8 stromal breast tumor from young Premenopausal


title: YA-BC-16 breast tumor from young adults Premenopausal


title: PB1 shoot sample grown in Phosphorus sufficient conditions biological rep. 2

description:
Gene expression data of 15 days old PB1 shoot tissue raised under Phosphporus sufficient condition
PB1 Shoot +P_2.CEL

source_name: 15-day-old whole seedling of PB1 unstressed

value: Phosphorus sufficient


title: MA-ES-2 stromal breast tumor from MA Posmenopausal


title: YA-BC-2 breast tumor from young adults Premenopausal


title: YA-ES-7 stromal breast tumor from young Premenopausal


title: PB1 shoot sample grown in Phosphorus sufficient conditions biological rep. 3

description:
Gene expression data of 15 days old PB1 shoot tissue raised under Phosphporus sufficient condition
PB1 Shoot +P_3.CEL


title: PB1 shoot sample grown in Phosphorus deficient conditions biological rep. 3

description:
Gene expression data of 15 days old PB1 shoot tissue raised under Phosphporus deficient condition
PB1 Shoot -P_3.CEL


title: YA-BC-12 breast tumor from young adults Premenopausal


title: MA-ES-4 stromal breast tumor from MA Posmenopausal


title: PB1 shoot sample grown in Phosphorus sufficient conditions biological rep. 1

description:
Gene expression data of 15 days old PB1 shoot tissue raised under Phosphporus sufficient condition
PB1 Shoot +P_1.CEL


title: MA-ES-3 stromal breast tumor from MA Posmenopausal


title: YA-BC-3 breast tumor from young adults Premenopausal


title: Blood1 CD8

description: replicate 1

value: CD8+ CLA+ CD45RO+


title: Dular shoot sample grown in Phosphorus deficient conditions biological rep. 3

description:
Gene expression data of 15 days old Dular shoot tissue raised under Phosphporus deficient condition
Dular Shoot -P_3.CEL

source_name: 15-day-old whole seedling of Dular stressed

value: Dular


title: Dular shoot sample grown in Phosphorus deficient conditions biological rep. 2

description:
Gene expression data of 15 days old Dular shoot tissue raised under Phosphporus deficient condition
Dular Shoot -P_2.CEL


title: Dular shoot sample grown in Phosphorus deficient conditions biological rep. 1

description:
Gene expression data of 15 days old Dular shoot tissue raised under Phosphporus deficient condition
Dular Shoot -P_1.CEL


title: Dular shoot sample grown in Phosphorus sufficient conditions biological rep. 3

description:
Gene expression data of 15 days old Dular shoot tissue raised under Phosphporus sufficient condition
Dular Shoot +P_3.CEL

source_name: 15-day-old whole seedling of Dular unstressed


title: Dular shoot sample grown in Phosphorus sufficient conditions biological rep. 2

description:
Gene expression data of 15 days old Dular shoot tissue raised under Phosphporus sufficient condition
Dular Shoot +P_2.CEL


title: PB1 root sample grown in Phosphorus deficient conditions biological rep. 3

description:
Gene expression data of 15 days old PB1 root tissue raised under Phosphporus deficient condition
PB1 Root -P_3.CEL


title: Dular shoot sample grown in Phosphorus sufficient conditions biological rep. 1

description:
Gene expression data of 15 days old Dular shoot tissue raised under Phosphporus sufficient condition
Dular Shoot +P_1.CEL


title: PB1 root sample grown in Phosphorus sufficient conditions biological rep. 2

description:
Gene expression data of 15 days old PB1 root tissue raised under Phosphporus sufficient condition
PB1 Root +P_2.CEL


title: Dular root sample grown in Phosphorus deficient conditions biological rep. 2

description:
Gene expression data of 15 days old Dular root tissue raised under Phosphporus deficient condition
Dular Root -P_2.CEL


title: PB1 root sample grown in Phosphorus deficient conditions biological rep. 2

description:
Gene expression data of 15 days old PB1 root tissue raised under Phosphporus deficient condition
PB1 Root -P_2.CEL


title: Dular root sample grown in Phosphorus deficient conditions biological rep. 1

description:
Gene expression data of 15 days old Dular root tissue raised under Phosphporus deficient condition
Dular Root -P_1.CEL


title: PB1 root sample grown in Phosphorus sufficient conditions biological rep. 3

description:
Gene expression data of 15 days old PB1 root tissue raised under Phosphporus sufficient condition
PB1 Root +P_3.CEL


title: Dular root sample grown in Phosphorus sufficient conditions biological rep. 1

description:
Gene expression data of 15 days old Dular root tissue raised under Phosphporus sufficient condition
Dular Root +P_1.CEL


title: Dular root sample grown in Phosphorus deficient conditions biological rep. 3

description:
Gene expression data of 15 days old Dular root tissue raised under Phosphporus deficient condition
Dular Root -P_3.CEL


title: PB1 root sample grown in Phosphorus deficient conditions biological rep. 1

description:
Gene expression data of 15 days old PB1 root tissue raised under Phosphporus deficient condition
PB1 Root -P_1.CEL


title: Dular root sample grown in Phosphorus sufficient conditions biological rep. 3

description:
Gene expression data of 15 days old Dular root tissue raised under Phosphporus sufficient condition
Dular Root +P_3.CEL


title: PB1 root sample grown in Phosphorus sufficient conditions biological rep. 1

description:
Gene expression data of 15 days old PB1 root tissue raised under Phosphporus sufficient condition
PB1 Root +P_1.CEL


title: Dular root sample grown in Phosphorus sufficient conditions biological rep. 2

description:
Gene expression data of 15 days old Dular root tissue raised under Phosphporus sufficient condition
Dular Root +P_2.CEL


title: genomic DNA from DIPG9-Hippocampus 2

type: genomic

city: Montreal

first: Nada

last: Jabado

state: QC

address: 1001 Décarie Boulevard

department: Department of Pediatrics

country: Canada

institute: McGill University

description: FFPE sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina 450k Human Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw data (idat files) generated by Illumina GenomeStudio Software were imported into R program and processed using minfi R package

label: Cy5 and Cy3

molecule: genomic DNA

source_name: DIPG9-Hippocampus 2

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from cells using QIAamp DNA FFPE Tissue kit or Qiagen DNeasy Kit according to standard instructions

tag: histone h3 mutations

value: WT

value: hippocampus


title: genomic DNA from DIPG9-Medulla 2

description: FFPE sample

source_name: DIPG9-Medulla 2

value: medulla


title: genomic DNA from DIPG9-Parietal Lobe 2

description: FFPE sample

source_name: DIPG9-Parietal Lobe 2

value: parietal lobe


title: genomic DNA from DIPG9-Thalamus 2

description: FFPE sample

source_name: DIPG9-Thalamus 2

value: thalmus


title: genomic DNA from DIPG9-Parietal Lobe 1

description: FFPE sample

source_name: DIPG9-Parietal Lobe 1


title: genomic DNA from DIPG9-Thalamus 1

description: FFPE sample

source_name: DIPG9-Thalamus 1


title: genomic DNA from DIPG9-Cerebellum 1

description: FFPE sample

source_name: DIPG9-Cerebellum 1

value: cerebellum


title: genomic DNA from DIPG9-Occipital Lobe 2

description: FFPE sample

source_name: DIPG9-Occipital Lobe 2

value: occipital lobe


title: genomic DNA from DIPG3-Pons 1

description: Frozen tissue

source_name: DIPG3-Pons 1

value: pons


title: genomic DNA from DIPG7-Ventricle 1

description: FFPE sample

source_name: DIPG7-Ventricle 1

value: ventricle


title: genomic DNA from DIPG9-Temporal Lobe 2

description: FFPE sample

source_name: DIPG9-Temporal Lobe 2

value: temporal lobe


title: genomic DNA from DIPG9-Cerebellum 2

description: FFPE sample

source_name: DIPG9-Cerebellum 2


title: genomic DNA from DIPG9-Occipital Lobe 1

description: FFPE sample

source_name: DIPG9-Occipital Lobe 1


title: genomic DNA from DIPG9-Hippocampus 1

description: FFPE sample

source_name: DIPG9-Hippocampus 1


title: genomic DNA from DIPG7-Temporal Lobe 1

description: FFPE sample

source_name: DIPG7-Temporal Lobe 1


title: genomic DNA from DIPG7-Frontal Lobe 2

description: FFPE sample

source_name: DIPG7-Frontal Lobe 2

value: frontal lobe


title: genomic DNA from DIPG7-Temporal Lobe 2

description: FFPE sample

source_name: DIPG7-Temporal Lobe 2


title: genomic DNA from DIPG7-Thalamus 2

description: FFPE sample

source_name: DIPG7-Thalamus 2


title: genomic DNA from DIPG9-Frontal Lobe 2

description: FFPE sample

source_name: DIPG9-Frontal Lobe 2


title: genomic DNA from DIPG3-Cerebrum

description: Frozen tissue


title: genomic DNA from DIPG7-Hippocampus 1

description: FFPE sample

source_name: DIPG7-Hippocampus 1


title: genomic DNA from DIPG7-Ventricle 2

description: FFPE sample

source_name: DIPG7-Ventricle 2


title: genomic DNA from DIPG7-Parietal Lobe 3

description: FFPE sample

source_name: DIPG7-Parietal Lobe 3


title: genomic DNA from DIPG7-Cerebellum 3

description: FFPE sample

source_name: DIPG7-Cerebellum 3


title: genomic DNA from DIPG3-Cerebellum

description: Frozen tissue


title: genomic DNA from DIPG3-Pons 2

description: Frozen tissue

source_name: DIPG3-Pons 2


title: genomic DNA from DIPG7-Cerebellum 4

description: FFPE sample

source_name: DIPG7-Cerebellum 4


title: genomic DNA from DIPG7-Pons 4

description: FFPE sample

source_name: DIPG7-Pons 4


title: genomic DNA from DIPG2-Temporal Lobe 1

description: FFPE sample

source_name: DIPG2-Temporal Lobe 1


title: genomic DNA from DIPG7-Parietal Lobe 2

description: FFPE sample

source_name: DIPG7-Parietal Lobe 2


title: genomic DNA from DIPG2-Frontal Lobe 1

description: FFPE sample

source_name: DIPG2-Frontal Lobe 1


title: genomic DNA from DIPG2-Pons 4

description: FFPE sample

source_name: DIPG2-Pons 4


title: genomic DNA from DIPG2-Cerebellum 6

description: FFPE sample

source_name: DIPG2-Cerebellum 6


title: genomic DNA from DIPG2-Frontal Lobe 2

description: FFPE sample

source_name: DIPG2-Frontal Lobe 2


title: B55125

city: Bethesda

first: David

last: McGaughey

state: MD

address: 50 South Drive Rm 5317

department: NHGRI

institute: NIH

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: minfi 1.8.9. Raw intensity data from minfi.

label: Cy3 and Cy5

source_name: Guthrie card spot

label_protocol: Not provided

extract_protocol: Not provided

tag: fas status

value: Control

tag: ethnicity

value: Black, NonHispanic

value: Male


title: B62382

value: Female


title: B53990

value: White, NonHispanic


title: B62253


title: B55335


title: B54521


title: B53679


title: B62321


title: B54602


title: B53779


title: B54553


title: B54450


title: B54178


title: B55270


title: B53330


title: genomic DNA from DIPG2-Cerebellum 5

description: FFPE sample

source_name: DIPG2-Cerebellum 5


title: B53325


title: B53477

value: Hispanic, White


title: B62212


title: B52997


title: B54759


title: B62049


title: B53285


title: B53321


title: B52341


title: B52639


title: B52273


title: B52626


title: B50435


title: B09879


title: B51013


title: B50819


title: B51283


title: B50299


title: B08543

value: Other


title: B50263


title: B51250


title: B54644


title: B09936


title: B50395


title: B51657


title: B09582


title: B09297


title: B09869


title: B09987


title: B07831


title: B08456


title: B06834


title: B09353


title: B08176


title: B50075


title: B51927


title: B08035


title: B09758


title: B07230


title: B06778


title: B07107


title: B07227


title: B06018


title: B08877


title: B05865


title: B05946


title: B03613


title: B00796


title: B06410


title: B03745


title: B05695


title: B06394


title: B00382


title: B04000


title: B03525


title: A38108

value: Case


title: A39244


title: A40627


title: A40764


title: A36607


title: A39840


title: A36949


title: JejunumWholeTissue, Male, d14, without antibiotic  ~ B18

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

description: Gene expression data of control  birds at day 14

hyb_protocol: Hybridization was performed as described in the One-Color Microarray-Based Gene Expression analyzis Low input Quick Amp Labelling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies). The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression analyzis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: The arrays were scanned using the DNA microarray scanner with Surescan high resolution Technology from Agilent Technologies. Agilent Scan Control with resolution of 5 µm, 16 bits and PMT of 100%. Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 colour gene expression.

data_processing: The data were analyzed by using R (v3.0.2) by executing different packages, including LIMMA (GENTLEMAN et al. 2005) and arrayQualityMetrics (KAUFFMANN et al. 2009). The data were read in and background corrected (method=normexp and offset=1) with functions from the R package LIMMA (GENTLEMAN et al. 2005) from Bioconductor (GENTLEMAN et al. 2004). Quantile normalization of the data was done between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes were removed in a three-step procedure, 1) get the highest of the dark spots to get a base value, 2) multiply by 1.1, and 3) the gene/probe must be expressed in each of the samples in the experimental condition.

organism: Gallus gallus

source_name: JejunumWholeTissue, Male, d14, without antibiotic (=control)

label_protocol: The input was 10 ng of total RNA and 600 ng of labelled cRNA was used for hybridization on the eight pack array (Agilent 049577 chicken array).

extract_protocol: Tissue samples were extracted from each animal and snap frozen in liquid nitrogen. Later samples were pooled.

treatment_protocol: Birds were divided into 2 groups, group 1: without antibiotic, group 2: with antibiotic (amoxicillin) administered at day1 in drinking water for 24hours

tag: strain

value: Jejunum

value: M

tag: day

tag: pool

tag: hatch

tag: treatment

value: without antibiotic


title: A37706


title: JejunumWholeTissue, Female, d14, without antibiotic  ~ B16

source_name: JejunumWholeTissue, Female, d14, without antibiotic (=control)

tag: tissue

value: F


title: A35720


title: A35751


title: JejunumWholeTissue, Male, d14, without antibiotic  ~ B17


title: JejunumWholeTissue, Male, d14, without antibiotic  ~ B20


title: B03416


title: JejunumWholeTissue, Female, d14, without antibiotic  ~ B13


title: B00506


title: JejunumWholeTissue, Male, d5, without antibiotic  ~ B10

description: Gene expression data of control  birds at day 5

source_name: JejunumWholeTissue, Male, d5, without antibiotic (=control)


title: JejunumWholeTissue, Male, d14, without antibiotic  ~ B19


title: JejunumWholeTissue, Male, d5, without antibiotic  ~ B11


title: JejunumWholeTissue, Female, d14, without antibiotic  ~ B14


title: JejunumWholeTissue, Male, d5, without antibiotic  ~ B12


title: JejunumWholeTissue, Female, d14, without antibiotic  ~ B15


title: JejunumWholeTissue, Female, d5, without antibiotic  ~ B8

source_name: JejunumWholeTissue, Female, d5, without antibiotic (=control)


title: A35174


title: A34303


title: B00858


title: JejunumWholeTissue, Female, d5, without antibiotic  ~ B7


title: A35358


title: A34569


title: A41135


title: JejunumWholeTissue, Female, d1, without antibiotic  ~ B3

description: Gene expression data of control  birds at day 1

source_name: JejunumWholeTissue, Female, d1, without antibiotic (=control)


title: JejunumWholeTissue, Female, d5, without antibiotic  ~ B5


title: JejunumWholeTissue, Male, d1, without antibiotic  ~ B2

source_name: JejunumWholeTissue, Male, d1, without antibiotic (=control)


title: A35050


title: JejunumWholeTissue, Male, d14, antibiotic ~ A19

description: Gene expression data of antibiotic treated birds at day 14

value: antibiotic


title: JejunumWholeTissue, Male, d14, antibiotic ~ A18


title: JejunumWholeTissue, Female, d5, without antibiotic  ~ B6


title: JejunumWholeTissue, Male, d1, without antibiotic  ~ B1


title: A35164


title: A33328


title: JejunumWholeTissue, Female, d14, antibiotic ~ A16


title: JejunumWholeTissue, Male, d14, antibiotic ~ A17


title: JejunumWholeTissue, Male, d5, without antibiotic  ~ B9


title: JejunumWholeTissue, Female, d14, antibiotic ~ A15


title: A33134


title: A33699


title: JejunumWholeTissue, Female, d14, antibiotic ~ A13


title: A34182


title: JejunumWholeTissue, Male, d5, antibiotic ~ A12

description: Gene expression data of antibiotic treated birds at day 5


title: JejunumWholeTissue, Male, d5, antibiotic ~ A10


title: JejunumWholeTissue, Male, d5, antibiotic ~ A9


title: JejunumWholeTissue, Female, d14, antibiotic ~ A14


title: JejunumWholeTissue, Female, d1, without antibiotic  ~ A4


title: JejunumWholeTissue, Female, d5, antibiotic ~ A5


title: JejunumWholeTissue, Female, d5, antibiotic ~ A7


title: JejunumWholeTissue, Female, d1, without antibiotic  ~ A3


title: JejunumWholeTissue, Female, d5, antibiotic ~ A6


title: JejunumWholeTissue, Female, d5, antibiotic ~ A8


title: A32642


title: A33401


title: JejunumWholeTissue, Male, d1, without antibiotic  ~ A1


title: A28326


title: A29901


title: JejunumWholeTissue, Male, d5, antibiotic ~ A11


title: A30503


title: A27829


title: A26886


title: A28986


title: JejunumWholeTissue, Male, d1, without antibiotic  ~ A2


title: A23467


title: A28126


title: A22227


title: A32982


title: A31241


title: A23510


title: A25857


title: A19082


title: A19654


title: A15367


title: WT cell at D15, biological rep2

city: Tian Jin

first: Yu

last: Yin

address: 94 Wei Jin Road

country: China

institute: Nankai University

description:
Sample name: WTD15-3
Genetic background: C57B6
Gene expression data from WT ESCs differentiated for 15 days.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.

organism: Mus musculus

source_name: WT cells differentiated for 15 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Undifferentiated ES cells were trypsinized to obtain a single cell suspension, and were cultured by using a hanging drop method. EBs were formed using EB medium, which is similar to ES cells medium except without LIF, and were cultured by using a hanging drop method. ES cells were cultivated of a definite number of cells in hanging drops as embryoid bodies for 4 days. 10-15 EBs were transferred to 6-well microwell plates per well for sample collection.

treatment_protocol: ES cells were trypsinized to single cell and washed by PBS. Differentiated cells were washed by PBS in wells.

tag: strain/background

tag: genotype/variation

value: WT

tag: cell type

value: differentiated embryonic stem cells

tag: stage of differentiation


title: KO cell at D15, biological rep2

description:
Sample name: KOD15-4
Genetic background: C57B6
Gene expression data from Terc KO ESCs differentiated for 15 days.

source_name: KO cells differentiated for 15 days

value: Terc-/-


title: A15072

tag: gender


title: A17607


title: A16016


title: A20138


title: Batch

city: Clermont Ferrand

first: Nadia

last: Gaci

state: Auvergne

address: 28, Place H. Dunant - B.P. 38

department: Pharmacy

institute: University d Auvergne

description:
Batch
raw data available in cy3 channel of file:
Batch_raw_data.txt

hyb_protocol: As published by Tottey et al, 2013

scan_protocol: Agilent Technologies, Palo Alto, CA

data_processing: PhylInterpret software

organism: uncultured bacterium

source_name: human fecal sample

label_protocol: As published by Tottey et al, 2013

growth_protocol: Fecal microbiota was grown in an anaerobic way in Macfarlane media.

extract_protocol: 16S bacterial genes amplified using universal primers, next labelled with Cy3 or Cy5 dyes and hybridized to the DNA microarray probes as stated before (Tottey et al, 2013).

treatment_protocol: Total DNA extracted using Qiagen Stool kit

tag: age (years)


title: KO cell at D15, biological rep1

description:
Sample name: KOD15-2
Genetic background: C57B6
Gene expression data from Terc KO ESCs differentiated for 15 days.


title: WT cell at D15, biological rep1

description:
Sample name: WTD15-1
Genetic background: C57B6
Gene expression data from WT ESCs differentiated for 15 days.


title: A18307


title: A15597


title: KO cell at D8, biological rep2

description:
Sample name: KOD8-4
Genetic background: C57B6
Gene expression data from Terc KO ESCs differentiated for 8 days.

source_name: KO cells differentiated for 8 days


title: A18725


title: Fecal sample

description:
Fecal sample
raw data available in cy5 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique7.txt


title: A13799


title: A19764


title: A13635


title: A23005


title: WT cell at D8, biological rep2

description:
Sample name: WTD8-3
Genetic background: C57B6
Gene expression data from WT ESCs differentiated for 8 days.

source_name: WT cells differentiated for 8 days


title: A13545


title: A16531


title: A13050


title: A11816


title: KO cell at D8, biological rep1

description:
Sample name: KOD8-2
Genetic background: C57B6
Gene expression data from Terc KO ESCs differentiated for 8 days.


title: Initial stabilization sample

description:
Initial stabilization sample
raw data available in cy3 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique7.txt


title: WT cell at D8, biological rep1

description:
Sample name: WTD8-1
Genetic background: C57B6
Gene expression data from WT ESCs differentiated for 8 days.


title: GLY+DMSO+PEG6

description:
Glycerol+DMSO+PEG preserved sample 6 months
raw data available in cy5 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique6.txt


title: A12279


title: A12853


title: GLY+DMSO+PEG3

description:
Glycerol+DMSO+PEG preserved sample 3 months
raw data available in cy3 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique6.txt


title: DMSO+PEG6

description:
DMSO+PEG preserved sample 6 months
raw data available in cy5 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique5.txt


title: KO cell at D0, biological rep2

description:
Sample name: A49P11
Genetic background: C57B6
Gene expression data from G3/4 Terc KO ESCs.

source_name: KO ES cells at passage 11

tag: cell line

value: undifferentiated embryonic stem cells


title: WT cell at D0, biological rep2

description:
Sample name: N33P12
Genetic background: C57B6
Gene expression data from WT ESCs.

source_name: WT ES cells at passage 12


title: A11512


title: DMSO+PEG3

description:
DMSO+PEG preserved sample 3 months
raw data available in cy3 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique5.txt


title: TM_KO_PE_4_RMA

city: Louisville

first: Tamer

middle: M

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

institute: University of Louisville

description: Gene expression data from PMCA4 Knockout fibroblasts treated with 30uM Phenyl Ephrine for 72 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G-4C (Affymetrix).

data_processing: The analysis was initially performed with MAS5.0 (Affymetrix) and Robust Multiarray Average (RMA) software as well as the software package PUMA (Propagating Uncertainty in Microarray Analysis)

source_name: PMCA4 KO fibroblasts treated with 30uM Phenyl Ephrine for 72 hours

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

growth_protocol: Fibroblasts were isolated and cultured  for 4 days at 37C in medium consists of 80% DMEM, 20% FBS, 1% Penicillin/streptomycin, 1% Fungizone, and 1% nonessential amino acids.

treatment_protocol: fibroblasts were wither treated or not with 30uM Phenyl Ephrine for 72 hours

tag: genotype

value: Knockout

tag: age

value: 3 month old mice

value: fibroblast


title: TM_KO_C_3_RMA

description: Gene expression data from PMCA4 Knockout fibroblasts.

source_name: PMCA4 KO fibroblasts

value: Male


title: WT cell at D0, biological rep1

description:
Sample name: N12P12
Genetic background: C57B6
Gene expression data from WT ESCs.


title: GLY+PEG6

description:
GLY+PEG preserved sample 6 months
raw data available in cy5 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique4.txt

value: Female


title: A11460

source_name: Guthrie card spot

tag: fas status

value: White, NonHispanic


title: TM_WT_PE_2_RMA

description: Gene expression data from PMCA4 WT fibroblasts treated with 30uM Phenyl Ephrine for 72 hours

value: Wild type


title: TM_WT_C_1_RMA

description: Gene expression data from PMCA4 WT fibroblasts.

source_name: PMCA4 WT fibroblasts


title: Ras cells rep2

city: Rehovot

first: Yonit

last: Hoffman

address: Herzel

country: Israel

institute: Weizmann Institute of Science

description: microRNAs

hyb_protocol: Hybridization was done for 20h with Agilent SurePrint G3 Unrestricted miRNA 8x60K (Release 19.0) arrays.

scan_protocol: Arrays were scanned using an Agilent DNA microarray scanner

data_processing: Arrays were analyzed using the AgiMicroRna package in R with the RMA algorithm.

source_name: WI-38 fast growers transformed by constitutively activated mutant H-RasV12 (“Ras”)

label_protocol: For each sample 100ng RNA was dephosphorylated, denatured, labeled with Cyanine 3-pCp and purified using Micro Bio-Spin 6 Columns.

growth_protocol: WI-38 cells were grown in 37° in MEM supplemented with 10% non-heat-inactivated fetal bovine serum (Sigma), pen-strep, sodium pyruvate, L-glutamine solution (Beit HaEmek).

extract_protocol: RNA was extracted using Nucleospin miRNA kit (Macherey-Nagel), according to manufacturer’s instructions.

treatment_protocol: no treatment


title: KO cell at D0, biological rep1

description:
Sample name: F35P11
Genetic background: C57B6
Gene expression data from G3/4 Terc KO ESCs.

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


title: T-ALL cells from LN3 thymic lymphoma, sample 3

city: Austin

first: Lauren

last: Ehrlich

state: TX

address: 2506 Speedway A5000

department: Molecular Biosciences

institute: The University of Texas at Austin

description:
T-ALL_LN3_3
FACS-sorted thymic dendritic cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G with GCOS version 1.4.0.036

data_processing: The data were normalized using the GC-RMA method on Gene Expression Commons (http://gexc.stanford.edu/)

source_name: T-ALL tumor cells from an LN3 thymic lymphoma

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol

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

value: LN3 thymic lymphoma

value: T-ALL tumor cells

tag: disease state

value: thymic lymphoma

value: LN3 (C57BL6 background)

value: 6 months

value: male


title: T-ALL cells from LN3 thymic lymphoma, sample 2

description:
T-ALL_LN3_2
FACS-sorted thymic dendritic cells

value: 4 months


title: Fast cells rep2

description: microRNAs

source_name: WI-38 fast growers (extensive passaging after immortalization)


title: GLY+PEG3

description:
GLY+PEG preserved sample 3 months
raw data available in cy3 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique4.txt


title: A10602

value: Case

tag: ethnicity


title: NEPC 4015-NA

city: Seattle

first: John

middle: K

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology Division

institute: Fred Hutchinson Cancer Research Center

description: Hybridized to CytoScan HD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were washed using Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Chromosome Analysis Suite (ChAS version 3.1.0.15).
Affymetrix CEL data file includes an intensity value, standard deviation of the intensity, and the number of pixels used to calculate the intensity value for each feature on the probe array.

source_name: NEPC 4015-NA

label_protocol: Per manufacturer's protocol.

growth_protocol: Tumors were grown subcutaneously in NSG mice. Cell line was grown in HITES media.

extract_protocol: Genomic DNA was extracted from homogenized cells using the Qiagen DNeasy Blood & Tissue Kit. DNA quality and quantity was evaluated using a Nanodrop Spectrophotometer and agarose gel electropheresis.

treatment_protocol: None.

value: NEPC

value: N-myc/myrAKT1 prostate tumor


title: T-ALL cells from LN3 thymic lymphoma, sample 1

description:
T-ALL_LN3_1
FACS-sorted thymic dendritic cells


title: Slow cells rep2

description: microRNAs

source_name: WI-38 slow growers (early passage after immortalization, Slow)


title: DMSO6

description:
DMSO preserved sample 6 months
raw data available in cy5 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique3.txt


title: DMSO3

description:
DMSO preserved sample 3 months
raw data available in cy3 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique3.txt


title: Control cells rep2

description: microRNAs

source_name: WI-38 primary fibroblasts (“Control”)


title: Sirpa+DC from LN3 thymic lymphoma, sample 2

description: FACS-sorted thymic dendritic cells

source_name: Sirpa+ dendritic cells from an LN3 thymic lymphoma

value: Sirpa+ dendritic cells


title: A10401


title: Sirpa+DC from LN3 thymic lymphoma, sample 3

description: FACS-sorted thymic dendritic cells


title: Sirpa+DC from LN3 thymic lymphoma, sample 1

description: FACS-sorted thymic dendritic cells


title: PEG6

description:
PEG preserved sample 6 months
raw data available in cy5 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique2.txt


title: A10596

value: Black, NonHispanic


title: NEPC 3882-NA

description: Hybridized to CytoScan HD

source_name: NEPC 3882-NA


title: NEPC 3045-NA

description: Hybridized to CytoScan HD

source_name: NEPC 3045-NA


title: Slow cells rep1

description: microRNAs


title: Gly6

description:
Glycerol preserved sample 6 months
raw data available in cy5 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique1.txt

source_name: human fecal sample


title: Fast cells rep1

description: microRNAs


title: PEG3

description:
PEG preserved sample 3 months
raw data available in cy3 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique2.txt


title: Sirpa-DC from LN3 thymic lymphoma, sample 3

description: FACS-sorted thymic dendritic cells

source_name: Sirpa- dendritic cells from an LN3 thymic lymphoma

value: Sirpa- dendritic cells


title: Gly3

description:
Glycerol preserved sample 3 months
raw data available in cy3 channel of file:
US91603675_256599410024_S01_CGH_105_Dec08_Classique1.txt


title: Pla2g10-Tg, thymus_Rep2

city: Setagaya

first: Kei

last: Yamamoto

state: Tokyo

address: 2-1-6 kamikitazawa

department: Lipid Metabolism Project

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

description: gene expression profile in thymus of Pla2g10-overexpressing transgenic mouse

hyb_protocol: 1.5 µg of Cy3 or Cy5-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 5 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with a Laser Scanner GenePix 4000B (Molecular Devices) using a scan resolution of 5µm and appropriate gains on the photomultiplier (PMT) to obtain the highest intensity without saturation.

data_processing: GenePix Software (Molecular Devices) was used for background subtraction and normalization.

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: Pla2g10-Tg/+ mice and littermate controls (C57BL/6 background) were housed in climate-controlled (23 oC) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard LFD (CE2; CLEA Japan) and water.

extract_protocol: Total RNA was extracted from thymus of 6-month old mouse and purified using the RNeasy Mini Kit (Qiagen). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

value: 6 month-old

tag: background strain

value: thymus

source_name: Control

value: Control


title: Sirpa-DC from LN3 thymic lymphoma, sample 2

description: FACS-sorted thymic dendritic cells


title: NEPC cell line LASCPC-01

description: Hybridized to CytoScan HD

source_name: NEPC cell line LASCPC-01

value: N-Myc/myrAKT1 prostate cell line LASCPC-01


title: Control cells rep1

description: microRNAs


title: A09631

value: Male


title: A09636

value: White, NonHispanic


title: Sirpa-DC from LN3 thymic lymphoma, sample 1

description: FACS-sorted thymic dendritic cells

value: LN3 thymic lymphoma

value: thymic lymphoma


title: A08883

value: Other


title: Pla2g10-Tg, thymus_Rep1


title: INF255_10749_1

status: Public on Jan 28 2016

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

data_processing: raw data were processed using the R/Bioconductor package limma for background correction and quantile normalization

label: cy dye

source_name: Biopsy

treatment_protocol: Colonoscopic pinch biopsies were collected from the sigmoid colon of patients with chronic active UC, chronic inactive UC, chronic active colonic CD, irritable bowel syndrome (IBS), infectious colitis (INF), and normal, healthy patients undergoing screening colonoscopies. Biopsies were placed immediately into 1 ml of TRIzol reagent (Invitrogen. Carlsbad, CA) and total RNA was extracted. The total RNAs were separated for into small and large RNA (> 200 nucleotides) fractions using the PureLink miRNA Isolation Kit (Invitrogen) and stored at -80°C.  The small RNA fraction was used in a previous study.  The large/long RNA fraction was used in this project.  The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile (Agilent Technologist. Santa Clara, CA)

tag: diagnosis

value: infectious colitis

tag: activity

value: active

tag: group

value: INF


title: Ras cells rep1

description: microRNAs


title: IBS184e_10769_2

value: irritable bowel syndrome

value: normal

value: IBS


title: CD84act2_10772_2

value: Crohn’s disease

value: aCD


title: IBS99_10771_1


title: A07627

value: Case

value: Black, NonHispanic

value: Female


title: A08424


title: IBS189_10770H_2


title: CD33act_110707_1


title: CD150act_10802_2


title: A08054


title: A08725


title: UC178act_10769_1

value: Ulcerative colitis

value: aUC


title: UC74act_110708_1


title: CD111act_10698_2


title: CD131act_10750_2


title: UC63act_0640_2


title: IBS96_110727_2


title: UC168act_10801_2


title: UC73act2_10772_1


title: UC169act_10753_2


title: A07449

value: White, NonHispanic

value: Male


title: UC161act_10803_2


title: UC143act_10755_2


title: UC71act_110711_2


title: UC153act_10751_2


title: UC148act_10752_1


title: UC144act_10758_2


title: A05706


title: A07358


title: UC139act_10697_2


title: UC90ina_110727_1

value: inactive

value: iUC


title: UC110act_10701_2


title: UC167act_10756_1


title: UC183ina_10757_2


title: UC87ina_110707_2


title: UC70ina_110708_2


title: UC93ina_10700_1


title: UC165ina_0649_2


title: UC130ina_10800_1


title: UC159ina_10756_2


title: UC118ina_10752_2


title: N234_10758_1

value: CTR


title: UC105ina_10661_1


title: N226_10803_1


title: UC127ina_10750_1


title: N66_0640_1


title: UC121ina_10802_1


title: UC109ina_10754_1


title: UC100ina_10698_1


title: N239_10757_1


title: A05761


title: N209_10753_1


title: N210_10751_1


title: N199_10755_1


title: N94_110711_1


title: IBS108_10771_2


title: N188_10701_1


title: N195_10697_1


title: N190_10699_1


title: INF157_10754_2

value: infectious colitis


title: N212_10801_1


title: N104_110710_1


title: N122_0649_1


title: INF156_10661_2

value: INF


title: DFO-Igm4-rep1

city: Shanghai

first: Yuhang

last: Jiang

address: 320 Yueyang Road

department: Institute of Health Sciences

institute: Shanghai Institutes for Biological Sciences, CAS

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Splenic B cells, Anti-IgM and DFO, 48h, replicate1

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Splenic B cells were cultured in 1640 medium with 10%(vol/vol) FBS, 0.05mM β-Mercaptoethanol, 1mM sodium pyruvate, 100U/ml penicillin and 100µg/ml streptomycin.

extract_protocol: RNA was prepared using the RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations. RNA quantity and quality were measured NanoDrop ND-1000. RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Pellet cells by centrifugation. Lyse cells in TRIzol Reagent by repetitive pipetting. Use 1 ml of the reagent per 5-10 × 106 of B cells. Washing cells before addition of TRIzol Reagent should be avoided as this increases the possibility of mRNA degradation

value: B cells

tag: tissue

value: spleen

value: male

tag: treatment

value: Anti-IgM stimulation for 48h (with DFO)


title: DFO-Lps6-rep1

source_name: Splenic B cells, LPS and DFO, 48h, replicate1

value: LPS stimulation for 48h (with DFO)


title: DFO-Med2-rep1

source_name: Splenic B cells, DFO, 48h, replicate1

value: 48hr in normal culture medium (with DFO)


title: Con-Lps5-rep1

source_name: Splenic B cells, LPS, 48h, replicate1

value: LPS stimulation for 48h


title: Con-Med1-rep1

source_name: Splenic B cells, control, 48h, replicate1

value: 48hr in normal culture medium


title: 145

city: salamanca

first: Juan

middle: Luis

last: Garcia

address: Campus Miguel de Unamuno

country: Spain

institute: Center Cancer Research

description: Muestra 155

hyb_protocol: Hybridization was performed according to the instructions in the NimbleGen Array User Guide

scan_protocol: Scanning was performed according to the instructions in the NimbleGen Array User Guide

data_processing: Arrays were processed using Nimblegen's standard protocol and segmented using the WAVICGH tool.

source_name: DNA from Colorectal cancer tissue

label_protocol: Samples were denatured and labeled in parallel with Cy3 for the test group and Cy5 for the control group, each through a random priming method, using Klenow fragments (NimbleGen Dual-Color DNA Labeling Kit, Roche NimbleGen, Inc., Madison, WI, USA)

extract_protocol: The genomic DNA was extracted from colo rectal cancer tissues  with QIAmp DNA Mini Kit (Qiagen,  16 Valencia, CA, USA) following the manufacturer’s instructions

tag: disease

value: Early-onset CRC

tag: age group

tag: genetic subtype

value: Not applicable

source_name: commercially available genomic DNA

tag: reference dna source

value: Human Genomic DNA, Female, Promega, Madison, WI, USA


title: 146

description: Muestra 156

tag: gender

value: Female

value: Human Genomic DNA, Male, Promega, Madison, WI, USA


title: Con-Igm3-rep1

source_name: Splenic B cells, Anti-IgM, 48h, replicate1

tag: cell type

value: Anti-IgM stimulation for 48h


title: 143

description: Muestra 151

value: Male


title: 144

description: Muestra 154


title: 136

description: Muestra 143


title: 140

description: Muestra 148


title: 127

description: Muestra 134


title: 126

description: Muestra 133


title: 128

description: Muestra 135


title: 139

description: Muestra 147


title: 135

description: Muestra 142


title: 125

description: Muestra 132


title: 137

description: Muestra 145


title: 132

description: Muestra 139


title: 142

description: Muestra 150


title: 131

description: Muestra 138


title: 138

description: Muestra 146


title: 133

description: Muestra 140


title: 129

description: Muestra 136


title: 124

description: Muestra 131


title: 134

description: Muestra 141


title: 141

description: Muestra 149


title: 130

description: Muestra 137


title: 122

description: Muestra 129


title: 121

description: Muestra 128


title: 119

description: Muestra 126


title: 123

description: Muestra 130


title: 120

description: Muestra 127


title: 117

description: Muestra 124


title: 116

description: Muestra 123


title: 114

description: Muestra 121


title: 115

description: Muestra 122


title: 113

description: Muestra 120


title: 112

description: Muestra 118


title: 111

description: Muestra 117


title: 103

description: Muestra 109


title: 109

description: Muestra 115


title: 108

description: Muestra 114


title: 96

description: Muestra 102


title: 100

description: Muestra 106


title: 97

description: Muestra 103


title: 105

description: Muestra 111


title: 110

description: Muestra 116


title: 102

description: Muestra 108


title: 106

description: Muestra 112


title: 94

description: Muestra 100


title: 107

description: Muestra 113


title: 98

description: Muestra 104


title: 118

description: Muestra 125


title: 99

description: Muestra 105


title: 104

description: Muestra 110-


title: 93

description: Muestra 98


title: INF246_10800_2

value: infectious colitis

value: normal


title: 90

description: Muestra 95


title: 92

description: Muestra 97


title: 88

description: Muestra 93


title: 101

description: Muestra 107-


title: 89

description: Muestra 94


title: 95

description: Muestra 101


title: 86

description: Muestra 89

value: Late-Onset Colorectal cancer


title: 84

description: Muestra 87


title: 82

description: Muestra 85


title: 81

description: Muestra 84


title: 76

description: Muestra 79


title: 91

description: Muestra 96


title: 85

description: Muestra 88


title: 80

description: Muestra 83


title: 79

description: Muestra 82


title: 77

description: Muestra 80


title: 87

description: Muestra 92


title: 83

description: Muestra 86


title: 78

description: Muestra 81


title: 73

description: Muestra 76


title: 75

description: Muestra 78


title: 64

description: Muestra 67


title: 66

description: Muestra 69-


title: PF_female gametocyte D12_Rep2

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

description:
raw data file: SG12454250_254853210016_S001_GE2_1105_Oct12_1_4.txt (Cy5 channel)
This sample is of Plasmodium falciparum female gametocyte at stage V. It is the second of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by Genomics Core Facility of Pennsylvania State University according to the manufacturer’s instructions (Agilent).

scan_protocol: Scanning was performed by Genomics Core Facility of Pennsylvania State University by using Axon GenePix 4000B.

data_processing: The raw data was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in DNASTAR software-ArrayStar 11 (dnastar.com).

source_name: Plasmodium falciparum, female gametocyte, D12, Rep2

label_protocol: Labeling was done by Genomics Core Facility of Pennsylvania State Univerity. Amplify 1ug of each sample using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit. Dye couple 15 ug of aRNA with Cy3 or Cy5 (GE Health Care #RPN5661), as appropriate, and subsequently purify according to the Ambion Kit instructions.(AM1753).

growth_protocol:
P. falciparum parasites were maintained as described previously (Trager and Jensen, 1976)
Induction of gametocytogenesis was performed as described (Fivelman et al., 2007).  Gametocytes were harvested at  Day 12 (stage V).

extract_protocol: The male and female gametocytes were separated by cell-sorter based on GFP intensity. Total RNA was extracted using the Trizol reagent (invirtogen.com)

tag: strain

value: Day 12

value: gametocyte


title: 67

description: Muestra 70


title: 74

description: Muestra 77


title: 71

description: Muestra 74


title: 62

description: Muestra 65


title: 63

description: Muestra 66


title: 61

description: muestra 64