title: AML [7187_15jan09]

description: Not Applicable


title: normal sample_42

status: Public on Jan 01 2013

type: RNA

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: RNA from peripheral blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of patients and volunteers without known disease was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). For each blood donor, 5 ml of peripheral blood were obtained. The content of blood sampling tubes of each patient_and healthy donor was centrifuged at 5000 g for 10 min at room temperature. The supernatant was discarded while the pellet was resuspended in 10 ml RNase free water by vortex. The suspension is again centrifuged at 5000 g for 10 min at RT. Subsequently, the total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden). Therefore the pellet was resuspended in 700 μl QIAzol lysis reagent and incubated for 5 min at RT. Then, 140 μl chloroform were added, vortexed for 15 sec, and incubated for 2-3 min at RT. This was followed by a centrifugation at 14000 rpm and 4°C for 15 min. The upper, watery phase was removed and 1,5 times of its volume added in 100% ethanol (ca. 900 μl). Each 700 μl of this mixture were placed on a column and centrifuged at 13000 rpm at RT for 15 sec. After the mixture had completely passed the column, 700 μl of Buffer RWT were added to each column, and again centrifuged at 13000 rpm at RT for 15 sec. Following this, 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 15 sec. After this, another 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 2 min. The column was then centrifuged at 13000 rpm and RT for 1 min to dry it. The following was the elution step with 40 μl RNase free water, centrifuging at 13000 rpm at RT for 1 min. The eluted RNA was stored at -70°C.

treatment_protocol: stored at -20 degree

tag: disease state

value: control


title: AML [7185_15jan09]

city: Rotterdam

first: Martin

middle: van

last: Vliet

address: Lichtenauerlaan 40

department: Bioinformatics

country: Netherlands

institute: SkylineDx

description: Not Applicable

hyb_protocol: As described in the AMLprofiler IFU (instructions for use), Hybridized for 17 hours, 45C at 60 rpm in Affymetrix Hybridization oven

scan_protocol: As described in the AMLprofiler IFU (instructions for use) on an Affymetrix GeneChip System 3000Dx v.2

data_processing: DM algorithm implemented in the Affymetrix Power Tools (APT 1.10.2).

label: Biotin

source_name: AML

label_protocol: We used 10 µg of total RNA to prepare antisense biotinylated RNA. Single-stranded complementary DNA (cDNA) and double-stranded cDNA were synthesized according to the manufacturer’s protocol (Invitrogen Life Technologies) with the use of the T7-(deoxythymidine)24-primer (Genset). In vitro transcription was performed with biotin-11-cytidine triphosphate and biotin-16-uridine triphosphate (Perkin–Elmer) and the MEGAScript T7 labeling kit (Ambion). Double-stranded cDNA and complementary RNA (cRNA) were purified and fragmented with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: Not Applicable

extract_protocol: After thawing, cells were washed once with Hanks’balanced-salt solution. High-quality total RNA was extracted by lysis with guanidinium thiocyanate followed by cesium chloride–gradient purification. RNA levels, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent). None of the samples showed RNA degradation (ratio of 28S ribosomal RNA to 18S ribosomal RNA of at least 2) or contamination by DNA.

treatment_protocol: Not Applicable

tag: cohort

value: Training

tag: npm1 status

value: NPM1 wt


title: AML [7186_23oct08]

description: Not Applicable

value: NPM1 A


title: 53 CD14B5_4403827073_E

city: Ulm

first: Nupur

last: Bhattacharya

address: Albert Einstein Allee 23

department: Department of Internal Medicine III

institute: University of Ulm

description: Healthy proband

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: differentiated CD14+ PBMCs from a healthy donor in coculture with non-malignant B cells

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

extract_protocol: RNA was extracted with  QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: age

value: above 50 years

tag: tissue

value: peripheral blood mononuclear cells

tag: cell type


title: 52 CD14B1_4403827073_D

description: Healthy proband


title: 58 NLC13_4403827073_J

description: CLL patient

source_name: differentiated CD14+ PBMCs from a CLL patient

value: NLC


title: normal sample_38


title: 51 NLC18_4403827073_C

description: CLL patient


title: 49 NLC16_4403827073_A

description: CLL patient


title: 50 NLC17_4403827073_B

description: CLL patient


title: genomic DNA from cervical smear  INVR6

type: genomic

city: Bogotá

first: Dabeiba

middle: Adriana

last: García Robayo

address: Carrera 7 No 40-62

department: Odontología

country: Colombia

institute: Pontificia Universidad Javeriana

description: Invasive carcinoma HPV positive types 16, 52

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
Illumina software GenomeStudio V2009.2 Methylation Module V1.5.5
Normalized data: The AVG_BETA value indicates the methylation level (beta) of each CpG dinucleotide.
Non-normalized data: Signal A and signal B are produced by two different bead types identifying the methylated and unmethylated versions of the CpG dinucleotide. See signal_intensities.txt (linked as a supplementary file on the Series record).

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated by phenol-chloroform method. The bisulfite conversion of genomic DNA was performed using the EZ Methylation Kit (Zymo Research, D5002).

tag: gender

value: Female

tag: sample type

value: cervical smear

value: Invasive cervical carcinoma


title: normal sample_37


title: normal sample_35


title: normal sample_36


title: normal sample_34


title: genomic DNA from cervical smear  INVD89

description: Invasive carcinoma HPV positive types 16, 18


title: normal sample_33


title: normal sample_31


title: normal sample_32


title: AML [7183_15jan09]

description: Not Applicable


title: AML [7178_15jan09]

description: Not Applicable


title: AML [7180_15jan09]

description: Not Applicable


title: AML [7177_15jan09]

description: Not Applicable


title: genomic DNA from cervical smear  INVD22

description: Invasive carcinoma HPV not determinated


title: AML [7172_15jan09]

description: Not Applicable


title: normal sample_30


title: normal sample_29


title: genomic DNA from cervical smear  ISD65

description: Carcinoma in situ HPV positive types 16, 18, 73

value: cervical carcinoma in situ


title: AML [7176_23oct08]

description: Not Applicable


title: AML [7169_15jan09]

description: Not Applicable


title: genomic DNA from cervical smear  ISD29

description: Carcinoma in situ HPV positive types 16, 18, 33


title: AML [7171_15jan09]

description: Not Applicable


title: normal sample_28


title: AML [7173_23oct08]

description: Not Applicable


title: genomic DNA from cervical smear  ISD30

description: Carcinoma in situ HPV not determinated


title: genomic DNA from cervical smear  ISD24

description: Carcinoma in situ HPV positive types 16, 18


title: AML [7168_23oct08]

description: Not Applicable


title: normal sample_25


title: normal sample_27


title: normal sample_26


title: AML [7167_15jan09]

description: Not Applicable


title: AML [7166_14jan09]

description: Not Applicable


title: genomic DNA from cervical smear  ISD72


title: genomic DNA from cervical smear  CIN2D58

description: Cervical intraepithelial neoplasia 2 HPV positive types 16, 18

value: Cervical intraepithelial neoplasia (CIN) 2


title: genomic DNA from cervical smear  CIN2F5

description: Cervical intraepithelial neoplasia 2 HPV positive types 6, 16, 18, 52, 56


title: genomic DNA from cervical smear  CIN2D52

description: Cervical intraepithelial neoplasia 2 HPV positive types 11, 16, 18, 52, 66


title: normal sample_24


title: genomic DNA from cervical smear  CIN2F10


title: AML [7164_23oct08]

description: Not Applicable


title: AML [7174_23oct08]

description: Not Applicable


title: genomic DNA from cervical smear  CIN1E50

description: Cervical intraepithelial neoplasia 1 HPV positive types 16, 18, 51

value: Cervical intraepithelial neoplasia (CIN) 1


title: genomic DNA from cervical smear  ISH20

description: Carcinoma in situ HPV positive types 16, 18, 69


title: normal sample_23


title: genomic DNA from cervical smear  CIN1T23

description: Cervical intraepithelial neoplasia 1 HPV positive types 16, 18, 53, 58


title: normal sample_21


title: normal sample_20


title: AML [7304_16jan09]

description: Not Applicable


title: normal sample_22


title: AML [7153_14jan09]

description: Not Applicable


title: genomic DNA from cervical smear  NEGD21

description: normal cervical sample HPV positive type 51

value: normal


title: AML [7150_23oct08]

description: Not Applicable


title: genomic DNA from cervical smear  CIN1E53

description: Cervical intraepithelial neoplasia 1 HPV positive types 11, 16, 18


title: AML [7151_14jan09]

description: Not Applicable


title: AML [7154_14jan09]

description: Not Applicable


title: AML [7148_14jan09]

description: Not Applicable


title: AML [7161_14jan09]

description: Not Applicable


title: genomic DNA from cervical smear  NEGT7

description: normal cervical sample HPV positive types 16, 18


title: normal sample_19


title: genomic DNA from cervical smear  NEGD51

description: normal cervical sample HPV positive type 16


title: AML [7149_14jan09]

description: Not Applicable


title: normal sample_18


title: AML [7147_14jan09]

description: Not Applicable


title: AML [7145_14jan09]

description: Not Applicable


title: AML [7146_14jan09]

description: Not Applicable


title: normal sample_14


title: normal sample_17


title: normal sample_13


title: normal sample_16


title: AML [7144_23oct08]

description: Not Applicable


title: normal sample_11


title: normal sample_15


title: AML [7142_14jan09]

description: Not Applicable


title: AML [7143_14jan09]

description: Not Applicable


title: normal sample_10


title: normal sample_12


title: AML [7137_14jan09]

description: Not Applicable


title: AML [7136_14jan09]

description: Not Applicable


title: normal sample_7


title: AML [7139_23oct08]

description: Not Applicable


title: normal sample_9


title: normal sample_3


title: normal sample_2


title: normal sample_1


title: AML [7128_13jan09]

description: Not Applicable


title: AML [7127_13jan09]

description: Not Applicable


title: AML [7131_13jan09]

description: Not Applicable

value: NPM1 non-ABD


title: AML [7125_23oct08]

description: Not Applicable

value: NPM1 D


title: AML [7122_13jan09]

description: Not Applicable


title: normal sample_4


title: AML [7121_23oct08]

description: Not Applicable


title: AML [7124_13jan09]

description: Not Applicable


title: normal sample_8


title: AML [7120_13jan09]

description: Not Applicable


title: AML [7134_13jan09]

description: Not Applicable


title: normal sample_5


title: AML [7118_13jan09]

description: Not Applicable


title: AML [7116_13jan09]

description: Not Applicable


title: AML [7119_13jan09]

description: Not Applicable


title: AML [7115_23oct08]

description: Not Applicable


title: AML [7117_13jan09]

description: Not Applicable


title: AML [7114_23oct08]

description: Not Applicable


title: AML [7078_08jan09]

description: Not Applicable


title: AML [7079_23oct08]

description: Not Applicable


title: Nrf2-/-/duodenal reflux replicate 2

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

country: USA

institute: Coriell Institute for Medical Research

description: Biological replicate 2 of 3 esophageal epithelium tissues of Nrf2-/- mouse with duodenal reflux

hyb_protocol: Cy3 or Cy5 labeled, linearly amplified cRNA samples were hybridized with Gene Expression Hybridization Kit (Agilent p/n 5188-5242) according to the user guide.

scan_protocol: Scanned on an Agilent Microarray Scanner p/n G2565BA

data_processing: Agilent Feature Extraction Software 9.1 was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: Esophageal epithelium of Nrf2-/- mouse with duodenal reflux

label_protocol: 1 µg of total RNA were labled with Agilent Low RNA Input Linear Amplification Kit, PLUS, Two-Color( Agilent p/n 5188-5340) according to the provided protocol.

extract_protocol:
The mice were bred in-house to generate embryos and offsprings of proper genotypes. Mice were PCR-genotyped according to protocols provided by the original developers.
Esophagi of wild-type and Nrf2-/- mice (12 weeks old ) without reflux or with gastric, duodenal or mixed reflux were dissected and snap-frozen for extraction of total RNA
Total RNA was extracted from mouse esophageal tissue using RNeasy Fibrous Tissue Mini Kit (Qiagen; Valencia, CA).

value: male

value: 12 weeks

value: whole esophagus

tag: strain

tag: genotype/variation

source_name: Agilent's Universal Mouse Reference RNA

tag: reference

value: 11 mouse cell lines


title: AML [7082_13jan09]

description: Not Applicable

value: Training

value: NPM1 wt


title: normal sample_6

value: control


title: AML [7081_23oct08]

description: Not Applicable


title: Nrf2-/-/mixed reflux replicate 2

description: Biological replicate 2 of 3 esophageal epithelium tissues of Nrf2-/- mouse with mixed reflux

source_name: Esophageal epithelium of Nrf2-/- mouse with mixed reflux

value: esophageal epithelium


title: Nrf2-/-/mixed reflux replicate 3

description: Biological replicate 3 of 3 esophageal epithelium tissues of Nrf2-/- mouse with mixed reflux


title: AML [7077_08jan09]

description: Not Applicable


title: Nrf2-/-/mixed reflux replicate 1

description: Biological replicate 1 of 3 esophageal epithelium tissues of Nrf2-/- mouse with mixed reflux


title: Nrf2-/-/duodenal reflux replicate 3

description: Biological replicate 3 of 3 esophageal epithelium tissues of Nrf2-/- mouse with duodenal reflux


title: AML [7076_08jan09]

description: Not Applicable


title: Nrf2-/-/duodenal reflux replicate 1

description: Biological replicate 1 of 3 esophageal epithelium tissues of Nrf2-/- mouse with duodenal reflux


title: Nrf2-/-/gastric reflux replicate 1

description: Biological replicate 1 of 3 esophageal epithelium tissues of Nrf2-/- mouse with gastric reflux

source_name: Esophageal epithelium of Nrf2-/- mouse with gastric reflux


title: Nrf2-/-/gastric reflux replicate 3

description: Biological replicate 3 of 3 esophageal epithelium tissues of Nrf2-/- mouse with gastric reflux


title: Nrf2-/-/without reflux replicate 3

description: Biological replicate 3 of 3 esophageal epithelium tissues of Nrf2-/- mouse without reflux

source_name: Esophageal epithelium of Nrf2-/- mouse without reflux


title: Wild-type/mixed reflux replicate 3

description: Biological replicate 3 of 3 esophageal epithelium tissues of C57BL/6J mouse with mixed reflux

source_name: Esophageal epithelium of C57BL/6J mouse with mixed reflux

value: wild type


title: Nrf2-/-/gastric reflux replicate 2

description: Biological replicate 2 of 3 esophageal epithelium tissues of Nrf2-/- mouse with gastric reflux


title: AML [7075_08jan09]

description: Not Applicable


title: Nrf2-/-/without reflux replicate 1

description: Biological replicate 1 of 3 esophageal epithelium tissues of Nrf2-/- mouse without reflux


title: Wild-type/mixed reflux replicate 2

description: Biological replicate 2 of 3 esophageal epithelium tissues of C57BL/6J mouse with mixedl reflux


title: Wild-type/mixed reflux replicate 1

description: Biological replicate 1 of 3 esophageal epithelium tissues of C57BL/6J mouse with mixed reflux


title: Nrf2-/-/without reflux replicate 2

description: Biological replicate 2 of 3 esophageal epithelium tissues of Nrf2-/- mouse without reflux


title: AML [7073_08jan09]

description: Not Applicable


title: Wild-type/duodenal reflux replicate 1

description: Biological replicate 1 of 3 esophageal epithelium tissues of C57BL/6J mouse with duodenal reflux

source_name: Esophageal epithelium of C57BL/6J mouse with duodenal reflux


title: Wild-type/duodenal reflux replicate 3

description: Biological replicate 3 of 3 esophageal epithelium tissues of C57BL/6J mouse with duodenal reflux


title: AML [7074_23oct08]

description: Not Applicable

value: NPM1 A


title: Wild-type/duodenal reflux replicate 2

description: Biological replicate 2 of 3 esophageal epithelium tissues of C57BL/6J mouse with duodenal reflux


title: AML [7071_08jan09]

description: Not Applicable


title: AML [7070_08jan09]

description: Not Applicable


title: AML [7067_08jan09]

description: Not Applicable


title: AML [7065_23oct08]

description: Not Applicable


title: AML [7063_23oct08]

description: Not Applicable


title: Wild-type/gastric reflux replicate 3

description: Biological replicate 3 of 3 esophageal epithelium tissues of C57BL/6J mouse with gastric reflux

source_name: Esophageal epithelium of C57BL/6J mouse with gastric reflux


title: AML [7072_08jan09]

description: Not Applicable


title: Wild-type/gastric reflux replicate 1

description: Biological replicate 1 of 3 esophageal epithelium tissues of C57BL/6J mouse with gastric reflux


title: DNA-UPPP-25

city: Baltimore

first: Michael

middle: F

last: Ochs

state: MD

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

institute: Johns Hopkins University

description: Sample name: 27714_5374669027_J

hyb_protocol: Chip process and data analysis were performed by using reagents provided in the kit and following manufacturer's manual.

scan_protocol: Data were extracted and summarized using BeadStudio v3.0 software.

data_processing: Data were analyzed in R from Illumina FinalReport files

label: C-Bio and A-DNP

source_name: Ctrl 125

label_protocol: Bisulfite conversion of genomic DNA was done with the EZ DNA methylation Kit (Zymo Research, D5002) by following manufacturer's protocol with modifications for Illumina Infinium Methylation Assay in the Johns Hopkins microarray core.

growth_protocol: human HNSCC and UPPP surgical samples

extract_protocol: DNA was extracted from all samples by digestion with 50 µg/mL proteinase K (Boehringer, Mannheim, Germany) in the presence of 1\% SDS at 48°C overnight, followed by phenol/chloroform extraction and ethanol precipitation.

treatment_protocol: human surgical specimens, flash frozen

tag: sample identifier

value: Ctrl 125

value: control (UPPP)


title: AML [7062_23oct08]

description: Not Applicable


title: AML [7061_08jan09]

description: Not Applicable


title: AML [7059_23oct08]

description: Not Applicable


title: Wild-type/without reflux replicate 1

description: Biological replicate 1 of 3 esophageal epithelium tissues of C57BL/6J mouse without reflux

source_name: Esophageal epithelium of C57BL/6J mouse without reflux


title: Wild-type/gastric reflux replicate 2

description: Biological replicate 2 of 3 esophageal epithelium tissues of C57BL/6J mouse with gastric reflux


title: DNA-CellLine_HCT116 DKO nonmethyl

description: Sample name: HCT116_non methyl_DKO_5337972005_L

source_name: HCT116 DKO nonmethyl

value: HCT116 DKO nonmethyl

value: cell line


title: Wild-type/without reflux replicate 2

description: Biological replicate 2 of 3 esophageal epithelium tissues of C57BL/6J mouse without reflux


title: DNA-UPPP-24

description: Sample name: 27706_5374669027_H

source_name: Ctrl 124

value: Ctrl 124

value: normal


title: DNA-CellLine_HCT116 full methyl

description: Sample name: HCT116_ full methyl_5337972008_L

source_name: HCT116 full methyl

value: HCT116 full methyl


title: AML [7058_08jan09]

description: Not Applicable


title: DNA-UPPP-22

description: Sample name: 27743_5374669036_K

source_name: Ctrl 122

value: Ctrl 122


title: Wild-type/without reflux replicate 3

description: Biological replicate 3 of 3 esophageal epithelium tissues of C57BL/6J mouse without reflux

value: male

value: 12 weeks


title: AML [7057_08jan09]

description: Not Applicable

source_name: AML


title: DNA-UPPP-21

description: Sample name: 27745_5374669036_B

source_name: Ctrl 121

value: Ctrl 121


title: DNA-UPPP-20

description: Sample name: 27741_5374669036_I

source_name: Ctrl 120

value: Ctrl 120


title: DNA-UPPP-23

description: Sample name: 27716_5374669027_L

source_name: Ctrl 123

value: Ctrl 123


title: DNA-UPPP-19

description: Sample name: 27773_5374669036_D

source_name: Ctrl 119

value: Ctrl 119


title: AML [7053_18dec08]

description: Not Applicable

value: Training

value: NPM1 wt


title: AML [7054_18dec08]

description: Not Applicable


title: AML [7055_18dec08]

description: Not Applicable


title: AML [7052_23oct08]

description: Not Applicable

value: NPM1 A


title: DNA-UPPP-18

description: Sample name: 25330_5374669012_D

source_name: Ctrl 118

value: Ctrl 118


title: MEF_xpo5_rep1

city: Freiburg

first: Yoko

middle: Fukuda

last: Yuzawa

address: Stübeweg 51

institute: Max-Planck Institute of Immunobiology

description: Gene expression after transfection of Exportin-5 siRNA

hyb_protocol: Hybridization and washing were done using Agilent Gene Expression Hybridization Kit (Agilent, 5188-5242) and Agilent Wash Buffer Kit (Agilent, 5188-5327) according to manufacturer's protocols (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5 May 2010).

scan_protocol: Slides were scanned after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Profile: AgilentHD_GX1col, Resolution: 5 μm).

data_processing: The scanned images were analyzed with Feature Extraction Software using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Further data processing was done using GeneSpring GX Software v11.0.

source_name: MEF cells, Exportin-5 siRNA transfeceted, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5, May 2010), followed by RNAeasy column purification (Qiagen, 4106).

growth_protocol: MEF cells were grown in DMEM medium containing 10% FCS and Anti-biotics at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the miRNeasy Kit (Qiagen, 217004) following the manufacturer's recommendations.  The protocol includes  on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: MEF cells were transfeceted with 60nM of siRNAs (negative control or targeting Exprotin-5) with reverse transfection using Lipofectamin RNAiMAX (invitrogen, 13778), and incubated for 12 hours. After incubation cells were starved by culturing in DMEM containing 0.2% FCS for 48 hours and re-fed with DMEM containing 20%FCS for 24 hours, along with second siRNA transfection (done by forward transfection).

tag: transfection

value: Exportin-5 siRNA transfeceted

value: Wild type primary mouse embryonic fibroblasts


title: AML [7163_14jan09]

description: Not Applicable


title: DNA-UPPP-17

description: Sample name: 25405_5374669012_L

source_name: Ctrl 117

value: Ctrl 117

value: control (UPPP)


title: MEF_xpo5_rep2

source_name: MEF cells, Exportin-5 siRNA transfeceted, replicate 2


title: DNA-UPPP-16

description: Sample name: 24098_5374669006_A

source_name: Ctrl 116

value: Ctrl 116

value: normal


title: AML [6981_18dec08]

description: Not Applicable


title: AML [7051_18dec08]

description: Not Applicable


title: AML [6982_18dec08]

description: Not Applicable


title: AML [6980_23oct08]

description: Not Applicable


title: DNA-UPPP-13

description: Sample name: 25317_5374669012_K

source_name: Ctrl 113

value: Ctrl 113


title: DNA-UPPP-15

description: Sample name: 24043_5374669005_J

source_name: Ctrl 115

value: Ctrl 115


title: DNA-UPPP-12

description: Sample name: 25374_5374669012_H

source_name: Ctrl 112

value: Ctrl 112


title: DNA-UPPP-08

description: Sample name: 25303_5374669012_G

source_name: Ctrl 108

value: Ctrl 108


title: MEF_nega_rep1

description: Gene expression after transfection of negative control siRNA

source_name: MEF cells, negative control siRNA transfeceted, replicate 1

value: negative control siRNA transfeceted


title: DNA-UPPP-10

description: Sample name: 25320_5374669012_B

source_name: Ctrl 110

value: Ctrl 110


title: MEF_nega_rep2

source_name: MEF cells, negative control siRNA transfeceted, replicate 2


title: AML [6979_23oct08]

description: Not Applicable

source_name: AML


title: AML [7056_23oct08]

description: Not Applicable


title: AML [6977_18dec08]

description: Not Applicable


title: DNA-UPPP-14

description: Sample name: 24060_5374669005_L

source_name: Ctrl 114

value: Ctrl 114


title: DNA-UPPP-09

description: Sample name: 25357_5374669012_F

source_name: Ctrl 109

value: Ctrl 109


title: DNA-UPPP-07

description: Sample name: 26385_5374669026_D

source_name: Ctrl 107

value: Ctrl 107


title: DNA-UPPP-11

description: Sample name: 25304_5374669012_I

source_name: Ctrl 111

value: Ctrl 111


title: AML [6974_18dec08]

description: Not Applicable

value: Training

value: NPM1 wt


title: DNA-UPPP-25

description: PHen-HNC-27714-1a-SNP6_0_(GenomeWideSNP_6).CEL

hyb_protocol: The labeled DNA was hybridized to the Affymetrix GeneChip Genome-Wide human SNP 6.0  arrays for 17hr at 50 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated DNA.  The staining was further amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.0 (AGCC v3.0) software from Affymetrix, using the standard default settings.

data_processing:
Analysis was performed in R with CRLMM package.
The processed data file (linked as supplementary file on Series record) comprises CNV estimation by gene provided as the average of CNV calls across gene region.

source_name: Ctrl 125

label_protocol: DNA samples were labeled following Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 User Guide and reagent from Affymetrix. Briefly, two aliqouts of 250 ng of high quality genomic DNA were subjected to Nsp I and Sty I digestion respectively.  Nsp I adaptor and Sty I adpator were then ligated to the corresponding digested DNA and diluted 1:4.  The resulting DNA were amplified by PCR using clonetech titanium PCR reagents and primer provided by Affymetrix.  The amplified DNA were combined and purified using Agencourt AMPure XP magnetic beads, fragmented, and labeled using Terminal DNA Transferase.

value: Ctrl 125


title: AML [6975_18dec08]

description: Not Applicable


title: DNA-UPPP-03

description: Sample name: 25616_5374669026_C

source_name: Ctrl 103

value: Ctrl 103


title: DNA-UPPP-22

description: PHen-HNC-27743-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 122

value: Ctrl 122

value: control (UPPP)


title: DNA-UPPP-23

description: PHen-HNC-27716-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 123

value: Ctrl 123

value: normal


title: DNA-UPPP-06

description: Sample name: 25620_5374669026_E

source_name: Ctrl 106

value: Ctrl 106


title: DNA-UPPP-24

description: PHen-HNC-27706-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 124

value: Ctrl 124


title: DNA-UPPP-21

description: PHen-HNC-27745-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 121

value: Ctrl 121


title: DNA-UPPP-20

description: PHen-HNC-27741-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 120

value: Ctrl 120


title: AML [6953_18dec08]

description: Not Applicable

value: NPM1 non-ABD


title: DNA-UPPP-19

description: PHen-HNC-27773-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 119

value: Ctrl 119


title: AML [6948_17dec08]

description: Not Applicable


title: AML [6949_17dec08]

description: Not Applicable


title: AML [6947_17dec08]

description: Not Applicable


title: AML [6952_23oct08]

description: Not Applicable

value: NPM1 A


title: AML [6955_18dec08]

description: Not Applicable


title: DNA-UPPP-01

description: Sample name: 25673_5374669026_I

source_name: Ctrl 101

value: Ctrl 101


title: DNA-HNSCC-48

description: Sample name: 18737_5374669005_E

source_name: Pt 48

value: Pt 48

value: tumor

value: HNSCC


title: DNA-UPPP-18

description: PHen-HNC-25330-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 118

value: Ctrl 118


title: DNA-HNSCC-50

description: Sample name: 25168_5374669006_H

source_name: Pt 50

value: Pt 50


title: AML [6945_17dec08]

description: Not Applicable

source_name: AML

value: Training

value: NPM1 wt


title: DNA-HNSCC-49

description: Sample name: 27217_5374669026_L

source_name: Pt 49

value: Pt 49


title: DNA-UPPP-02

description: Sample name: 28627_5374669036_F

source_name: Ctrl 102

value: Ctrl 102

value: normal

value: control (UPPP)


title: DNA-HNSCC-47

description:
Sample name: 27253_5374669027_G
Sample name: poor cellulosity

source_name: Pt 47

value: Pt 47


title: DNA-UPPP-04

description: Sample name: 26131_5374669026_B

source_name: Ctrl 104

value: Ctrl 104


title: DNA-UPPP-16

description: PHen-HNC-24098-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 116

value: Ctrl 116


title: DNA-UPPP-17

description: PHen-HNC-25405-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 117

value: Ctrl 117


title: DNA-HNSCC-46

description: Sample name: 25170_5374669006_J

source_name: Pt 46

value: Pt 46


title: DNA-HNSCC-45

description: Sample name: 27729_5374669036_E

source_name: Pt 45

value: Pt 45


title: DNA-UPPP-15

description: PHen-HNC-24043-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 115

value: Ctrl 115


title: DNA-UPPP-14

description: PHen-HNC-24060-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 114

value: Ctrl 114


title: DNA-UPPP-13

description: PHen-HNC-25317-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 113

value: Ctrl 113


title: AML [6890_23oct08]

description: Not Applicable


title: AML [6891_23oct08]

description: Not Applicable


title: AML [6892_23oct08]

description: Not Applicable


title: DNA-UPPP-12

description: PHen-HNC-25374-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 112

value: Ctrl 112


title: DNA-UPPP-10

description: PHen-HNC-25320-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 110

value: Ctrl 110


title: AML [6887_17dec08]

description: Not Applicable

value: Training


title: AML [6888_17dec08]

description: Not Applicable

value: NPM1 wt


title: AML [6889_22oct08]

description: Not Applicable


title: DNA-UPPP-09

description: PHen-HNC-25357-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 109

value: Ctrl 109


title: AML [6884_17dec08]

description: Not Applicable


title: AML [6885_22oct08]

description: Not Applicable

value: NPM1 A


title: DNA-UPPP-08

description: PHen-HNC-25303-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 108

value: Ctrl 108

value: normal


title: DNA-UPPP-07

description: PHen-HNC-26385-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 107

value: Ctrl 107

value: control (UPPP)


title: DNA-HNSCC-44

description: Sample name: 27738_5374669036_G

source_name: Pt 44

value: Pt 44

value: tumor

value: HNSCC


title: AML [6883_10dec08]

description: Not Applicable

source_name: AML


title: DNA-HNSCC-40

description: Sample name: 23525_5374669005_K

source_name: Pt 40

value: Pt 40


title: AML [6882_10dec08]

description: Not Applicable


title: DNA-UPPP-06

description: PHen-HNC-25620-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 106

value: Ctrl 106


title: DNA-UPPP-11

description: PHen-HNC-25304-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 111

value: Ctrl 111


title: DNA-HNSCC-41

description:
Sample name: 1809_TDNA_5374669036_L
Sample name: poor cellulosity

source_name: Pt 41

value: Pt 41


title: DNA-HNSCC-42

description: Sample name: 25815_5374669026_K

source_name: Pt 42

value: Pt 42


title: DNA-HNSCC-37

description: Sample name: 24887_5374669006_D

source_name: Pt 37

value: Pt 37


title: DNA-HNSCC-43

description: Sample name: 27231_5374669027_C

source_name: Pt 43

value: Pt 43


title: DNA-HNSCC-39

description: Sample name: 27718_5374669036_A

source_name: Pt 39

value: Pt 39


title: DNA-HNSCC-38

description:
Sample name: 24886_5374669006_B
Sample name: poor cellulosity

source_name: Pt 38

value: Pt 38


title: DNA-HNSCC-35

description:
Sample name: 1683_TDNA_5337972008_F
Sample name: poor cellulosity

source_name: Pt 35

value: Pt 35


title: AML [6880_10dec08]

description: Not Applicable

value: Training

value: NPM1 wt


title: AML [6881_22oct08]

description: Not Applicable


title: AML [6735_10dec08]

description: Not Applicable


title: DNA-HNSCC-34

description: Sample name: 25258_5374669006_L

source_name: Pt 34

value: Pt 34


title: AML [6734_10dec08]

description: Not Applicable


title: DNA-UPPP-02

description: PHen-HNC-25671-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 102

value: Ctrl 102

value: normal

value: control (UPPP)


title: AML [6732_10dec08]

description: Not Applicable

value: NPM1 A


title: AML [6730_22oct08]

description: Not Applicable


title: AML [6724_22oct08]

description: Not Applicable

value: NPM1 D


title: DNA-HNSCC-36

description: Sample name: 2104_TDNA_5374669055_A

source_name: Pt 36

value: Pt 36

value: tumor

value: HNSCC


title: DNA-HNSCC-33

description:
Sample name: 27201_5374669026_J
Sample name: poor cellulosity

source_name: Pt 33

value: Pt 33


title: DNA-UPPP-05

description: PHen-HNC-25397-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 105

value: Ctrl 105


title: DNA-HNSCC-49

description: PHen-HNC-27217-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 49

value: Pt 49


title: DNA-UPPP-04

description: PHen-HNC-26131-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 104

value: Ctrl 104


title: DNA-HNSCC-50

description: PHen-HNC-25168-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 50

value: Pt 50


title: AML [6723_10dec08]

description: Not Applicable

source_name: AML


title: DNA-HNSCC-32

description: Sample name: 26856_5374669026_F

source_name: Pt 32

value: Pt 32


title: DNA-UPPP-03

description: PHen-HNC-25616-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 103

value: Ctrl 103


title: AML [6721_10dec08]

description: Not Applicable

value: Training

value: NPM1 wt


title: DNA-HNSCC-48

description: PHen-HNC-18737-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 48

value: Pt 48


title: DNA-HNSCC-28

description: Sample name: 23809_5374669005_B

source_name: Pt 28

value: Pt 28


title: DNA-HNSCC-30

description: Sample name: 27279_5374669027_D

source_name: Pt 30

value: Pt 30


title: DNA-HNSCC-31

description: Sample name: 26859_5374669026_H

source_name: Pt 31

value: Pt 31


title: DNA-HNSCC-46

description: PHen-HNC-25170-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 46

value: Pt 46


title: AML [6719_22oct08]

description: Not Applicable


title: AML [6720_10dec08]

description: Not Applicable


title: DNA-UPPP-01

description: PHen-HNC-25673-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Ctrl 101

value: Ctrl 101

value: normal

value: control (UPPP)


title: DNA-HNSCC-45

description: PHen-HNC-27729-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 45

value: Pt 45

value: tumor

value: HNSCC


title: DNA-HNSCC-27

description:
Sample name: 27940_5374669036_H
Sample name: poor cellulosity

source_name: Pt 27

value: Pt 27


title: AML [6717_22oct08]

description: Not Applicable


title: DNA-HNSCC-44

description: PHen-HNC-27738-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 44

value: Pt 44


title: DNA-HNSCC-43

description: PHen-HNC-27231-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 43

value: Pt 43


title: DNA-HNSCC-42

description: PHen-HNC-25815-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 42

value: Pt 42


title: DNA-HNSCC-29

description: Sample name: 27218_5374669027_A

source_name: Pt 29

value: Pt 29


title: DNA-HNSCC-40

description: PHen-HNC-23525-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 40

value: Pt 40


title: DNA-HNSCC-25

description: Sample name: 28680_5374669026_G

source_name: Pt 25

value: Pt 25


title: DNA-HNSCC-26

description: Sample name: 24100_5374669006_C

source_name: Pt 26

value: Pt 26


title: DNA-HNSCC-24

description: Sample name: 27281_5374669027_F

source_name: Pt 24

value: Pt 24


title: DNA-HNSCC-39

description: PHen-HNC-27718-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 39

value: Pt 39


title: DNA-HNSCC-37

description: PHen-HNC-24887-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 37

value: Pt 37


title: DNA-HNSCC-36

description: PHen-HNC-2104_TDNA-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 36

value: Pt 36


title: AML [6464_22oct08]

description: Not Applicable

source_name: AML

value: Training

value: NPM1 wt


title: AML [6463_09dec08]

description: Not Applicable


title: DNA-HNSCC-23

description: Sample name: 25283_5374669012_C

source_name: Pt 23

value: Pt 23


title: AML [6465_09dec08]

description: Not Applicable

value: NPM1 non-ABD


title: AML [6462_09dec08]

description: Not Applicable


title: AML [6715_10dec08]

description: Not Applicable


title: AML [6461_09dec08]

description: Not Applicable


title: AML [6976_18dec08]

description: Not Applicable


title: DNA-HNSCC-20

description: Sample name: 27259_5374669027_K

source_name: Pt 20

value: Pt 20

value: tumor

value: HNSCC


title: DNA-HNSCC-32

description: PHen-HNC-26856-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 32

value: Pt 32


title: DNA-HNSCC-21

description: Sample name: 24635_5374669006_I

source_name: Pt 21

value: Pt 21


title: DNA-HNSCC-19

description: Sample name: 23817_5374669005_D

source_name: Pt 19

value: Pt 19


title: DNA-HNSCC-18

description: Sample name: 25260_5374669012_A

source_name: Pt 18

value: Pt 18


title: AML [6459_09dec08]

description: Not Applicable


title: DNA-HNSCC-34

description: PHen-HNC-25258-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 34

value: Pt 34


title: AML [6714_10dec08]

description: Not Applicable


title: DNA-HNSCC-22

description: Sample name: 24642_5374669006_K

source_name: Pt 22

value: Pt 22


title: DNA-HNSCC-17

description: Sample name: 27248_5374669027_E

source_name: Pt 17

value: Pt 17


title: AML [6458_09dec08]

description: Not Applicable


title: DNA-HNSCC-16

description: Sample name: 18732_5374669005_C

source_name: Pt 16

value: Pt 16


title: DNA-HNSCC-30

description: PHen-HNC-27279-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 30

value: Pt 30


title: DNA-HNSCC-31

description: PHen-HNC-26859-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 31

value: Pt 31


title: DNA-HNSCC-15

description: Sample name: 2934_TDNA_5374669055_C

source_name: Pt 15

value: Pt 15


title: AML [6457_22oct08]

description: Not Applicable

value: Training

value: NPM1 wt


title: DNA-HNSCC-29

description: PHen-HNC-27218-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 29

value: Pt 29


title: DNA-HNSCC-14

description: Sample name: 24386_5374669006_E

source_name: Pt 14

value: Pt 14


title: AML [6456_22oct08]

description: Not Applicable

value: NPM1 A


title: DNA-HNSCC-28

description: PHen-HNC-23809-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 28

value: Pt 28

value: tumor

value: HNSCC


title: DNA-UPPP-05

description: Sample name: 25397_5374669012_J

source_name: Ctrl 105

value: Ctrl 105

value: normal

value: control (UPPP)


title: DNA-HNSCC-13

description: Sample name: 25133_5374669006_F

source_name: Pt 13

value: Pt 13


title: DNA-HNSCC-24

description: PHen-HNC-27281-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 24

value: Pt 24


title: DNA-HNSCC-25

description: PHen-HNC-27788-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 25

value: Pt 25


title: AML [6455_09dec08]

description: Not Applicable

source_name: AML


title: AML [6454_09dec08]

description: Not Applicable


title: DNA-HNSCC-23

description: PHen-HNC-25283-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 23

value: Pt 23


title: AML [6450_05dec08]

description: Not Applicable


title: AML [6451_05dec08]

description: Not Applicable


title: DNA-HNSCC-22

description: PHen-HNC-24642-1a-SNP6_0_(GenomeWideSNP_6).CEL

value: Pt 22


title: AML [6448_05dec08]

description: Not Applicable


title: AML [6449_22oct08]

description: Not Applicable


title: AML [6453_22oct08]

description: Not Applicable


title: DNA-HNSCC-11

description: Sample name: 23869_5374669005_F

source_name: Pt 11

value: Pt 11


title: DNA-HNSCC-21

description: PHen-HNC-24635-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 21

value: Pt 21


title: DNA-HNSCC-20

description: PHen-HNC-27259-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 20

value: Pt 20


title: DNA-HNSCC-26

description: PHen-HNC-24100-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 26

value: Pt 26


title: DNA-HNSCC-12

description: Sample name: 20597_5374669005_I

source_name: Pt 12

value: Pt 12


title: DNA-HNSCC-19

description: PHen-HNC-23817-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 19

value: Pt 19


title: DNA-HNSCC-10

description: Sample name: 7746_5374669005_A

source_name: Pt 10

value: Pt 10


title: AML [6378_05dec08]

description: Not Applicable

value: Training

value: NPM1 wt


title: AML [6376_05dec08]

description: Not Applicable


title: DNA-HNSCC-18

description: PHen-HNC-25260-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 18

value: Pt 18

value: tumor

value: HNSCC


title: DNA-HNSCC-08

description: Sample name: 24511_5374669006_G

source_name: Pt 8

value: Pt 8


title: DNA-HNSCC-09

description: Sample name: 25414_5374669026_A

source_name: Pt 9

value: Pt 9


title: DNA-HNSCC-16

description: PHen-HNC-18732-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 16

value: Pt 16


title: AML [6374_22oct08]

description: Not Applicable

value: NPM1 B


title: DNA-HNSCC-05

description: Sample name: 25300_5374669012_E

source_name: Pt 5

value: Pt 5


title: DNA-HNSCC-15

description: PHen-HNC-2934_TDNA-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 15

value: Pt 15


title: DNA-HNSCC-07

description: Sample name: 20416_5374669005_G

source_name: Pt 7

value: Pt 7


title: DNA-HNSCC-06

description: Sample name: 3679_TDNA_5374669055_E

source_name: Pt 6

value: Pt 6


title: DNA-HNSCC-04

description: Sample name: 27254_5374669027_I

source_name: Pt 4

value: Pt 4


title: AML [6379_05dec08]

description: Not Applicable

source_name: AML

value: NPM1 A


title: DNA-HNSCC-02

description: Sample name: 27728_5374669036_C

source_name: Pt 2

value: Pt 2


title: DNA-HNSCC-01

description: Sample name: 23877_5374669005_H

source_name: Pt 1

value: Pt 1


title: DNA-HNSCC-14

description: PHen-HNC-24386-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 14

value: Pt 14


title: DNA-HNSCC-03

description: Sample name: 27272_5374669027_B

source_name: Pt 3

value: Pt 3


title: AML [6373_05dec08]

description: Not Applicable

value: Training

value: NPM1 wt


title: AML [6372_22oct08]

description: Not Applicable


title: DNA-HNSCC-13

description: PHen-HNC-25133-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 13

value: Pt 13

value: tumor

value: HNSCC


title: AML [6371_28nov08]

description: Not Applicable


title: DNA-HNSCC-12

description: PHen-HNC-20597-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 12

value: Pt 12


title: AML [6370_28nov08]

description: Not Applicable


title: DNA-HNSCC-17

description: PHen-HNC-27248-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 17

value: Pt 17


title: AML [6375_22oct08]

description: Not Applicable


title: AML [6369_28nov08]

description: Not Applicable


title: DNA-HNSCC-11

description: PHen-HNC-23869-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 11

value: Pt 11


title: DNA-HNSCC-10

description: PHen-HNC-7746-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 10

value: Pt 10


title: DNA-HNSCC-09

description: PHen-HNC-25414-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 9

value: Pt 9


title: DNA-HNSCC-08

description: PHen-HNC-24511-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 8

value: Pt 8


title: DNA-HNSCC-06

description: PHen-HNC-3679_TDNA-1a-SNP6_0_(GenomeWideSNP_6).CEL

value: Pt 6


title: DNA-HNSCC-07

description: PHen-HNC-20416-1a-SNP6_0_(GenomeWideSNP_6).CEL

value: Pt 7


title: DNA-HNSCC-05

description: PHen-HNC-25300-1a-SNP6_0_(GenomeWideSNP_6).CEL

source_name: Pt 5

value: Pt 5


title: DNA-HNSCC-04

description: PHen-HNC-27254-1a-SNP6_0_(GenomeWideSNP_6).CEL

value: Pt 4


title: DNA-HNSCC-03

description: PHen-HNC-27272-1a-SNP6_0_(GenomeWideSNP_6).CEL


title: DNA-HNSCC-02

description: PHen-HNC-27728-1a-SNP6_0_(GenomeWideSNP_6).CEL

value: Pt 2


title: AML [6360_21oct08]

description: Not Applicable


title: AML [6359_28nov08]

description: Not Applicable


title: AML [6362_28nov08]

description: Not Applicable

value: NPM1 A


title: AML [6361_28nov08]

description: Not Applicable

value: Training


title: AML [6368_28nov08]

description: Not Applicable


title: DNA-HNSCC-01

description: PHen-HNC-23877-1a-SNP6_0_(GenomeWideSNP_6).CEL

value: Pt 1


title: AML [6364_28nov08]

description: Not Applicable

value: NPM1 wt


title: AML [6366_28nov08]

description: Not Applicable


title: AML [6363_21oct08]

description: Not Applicable


title: AML [6365_22oct08]

description: Not Applicable


title: AML [6367_28nov08]

description: Not Applicable


title: AML [6358_28nov08]

description: Not Applicable


title: Genome DNA from RKO cells treated with SRCAP siRNA and 5-Aza-CdR for 72hr

city: Detroit

first: Houtan

last: Noushmehr

state: MI

address: 2799 W. Grand Blvd

institute: Henry Ford Health System

description: Colon cancer cell line sample

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

data_processing: In house script, see Noushmehr H. Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma. Cancer Cell. 17(5): 510-22, 2010.

growth_protocol: RKO cell line is purchased from ATCC and cultured in MEM mediun with 10%FBS.

extract_protocol: Genomic DNA was extracted and purified from treated RKO cells using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: RKO cells are treated with non target or SRCAP siRNA 100nM for 24hrs and  followed by 1uM 5-Aza-CdR or PBS for 72hrs.

tag: cell line

value: RKO

tag: treatment

value: SRCAP siRNA and 5-Aza-CdR for 72hr


title: Udorn-PR8 HA 2

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

institute: Utrecht University

description: Gene expression in middle ear tissue of 6 days post infection with IAV - Udorn with PR8 HA

hyb_protocol: Performed according to NimbleGen protocols

scan_protocol: Array images were acquired with a NimbleGen MS200 scanner following their standard operation protocol, using the autogain function per subarray.

data_processing: The raw data images were processed with NimbleScan software. RMA normalization and background correction was used as implemented in the ArrayStar software package (DNAstar inc.)

source_name: auris media

growth_protocol: Five-day old C57BL/6 mice were colonised intranasally (i.n.) with 2×103 colony forming units (CFU) of  S. pneumoniae EF3030Lux in 3 µLs of PBS. Alternatively, mice were mock-infected with an equivalent volume of phosphate buffered saline (PBS). At 14-days of age, infant mice were infected i.n. with 20 plaque forming units (PFU) (PR8/34, Cambridge/34 and WSN/33) or 102.5 PFU (all other virus strains) of egg-grown IAV in 3 µLs of PBS. Viral doses were selected to ensure a reproducible infection with minimum morbidity and no mortality. Six days post-IAV infection, mice were euthanised and organs were collected for analysis.

extract_protocol: RNA was extracted using Trizol (Invitrogen, USA), purified using the RNAeasy minielute kit (Qiagen, USA) and DNA-se treated (Turbo DNase treatment; Ambion, USA).

treatment_protocol: Six independent biological replicates (where both ears from one mouse were pooled to create one sample) were used for each condition

tag: infection

value: Udorn-PR8 HA

value: middle ear


title: Udorn-PR8 HA 6

label_protocol: Performed according to NimbleGen protocols


title: Genome DNA from RKO cells treated with SRCAP siRNA and PBS for 72hr

description: Colon cancer cell line sample

value: SRCAP siRNA and PBS for 72hr


title: Genome DNA from RKO cells treated with Non-target siRNA and 5-Aza-CdR for 72hr

description: Colon cancer cell line sample

value: Non-target siRNA and 5-Aza-CdR for 72hr


title: Udorn3

description: Gene expression in middle ear tissue of mice 6 days post infection with IAV - Udorn

value: Udorn


title: Udorn-PR8 HA 1


title: M3

city: Boston

first: Matija

last: Snuderl

state: MA

address: 55 Fruit St.

department: Pathology

institute: MAssachusetts General Hospital

description: comparison between MBL and normal genomic DNA

hyb_protocol: The labeled DNA were purified with the Millipore Amicon 30 kDa centrifugal filter device (Billerica, MA) and mixed in equal proportion for hybridization to the array in the presence of Cot-1 DNA (Invitrogen, Carlsbad, CA) using the Agilent Oligo aCGH Hybridization Kit.

scan_protocol: Washed slides were scanned using the Agilent G2565CA Microarray Scanner.  Microarray TIFF (.tif)

data_processing: Images were processed and analyzed with Agilent CytoGenomics v1.5 software.

source_name: Tumor

label_protocol: Control and tumor DNA were labeled by random priming with CY3- and CY5-dUTP dyes, respectively using the Agilent Genomic DNA Enzymatic Labeling Kit.

extract_protocol: Genomic DNA was extracted from formalin-fixed, paraffin-embedded tissue using the QIAamp Blood Mini Kit using a modified protocol incorporating deparaffinization and protease digestion (QIAGEN, Valencia, CA).

value: Medulloblastoma

source_name: Control

value: blood

value: male


title: Udorn-PR8 HA 5


title: Udorn5


title: Udorn6


title: Udorn-PR8 HA 3


title: M13


title: Genome DNA from RKO cells treated with Non-target siRNA and PBS for 72hr

description: Colon cancer cell line sample

value: Non-target siRNA and PBS for 72hr


title: AML [6356_20jan09]

description: Not Applicable


title: Udorn4


title: Udorn-PR8 HA 4


title: CosR-knockdown replicate 2.

city: Seoul

first: Sunyoung

last: Hwang

address: 599 Gwanak-ro

department: Department of Food and Animal Biotechnology

country: South Korea

institute: Seoul National University

description: Biological replication 2 of 3

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring 7.3.1 (Agilent Technologies, USA).

organism: Campylobacter jejuni

source_name: C. jejuni wild type

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for CosR-knockdown) or Cy3-dUTP (for the wild type).

growth_protocol: C. jejuni cells adjusted final OD value to 0.08 at 600 nm were grown at 42°C in MH broth to the mid-exponential phase for approximately 8 hr with shaking under microaerphilic condition.

extract_protocol: The total RNA was extracted with Trizol reagent (Invitrogen) according to the manufacturer’s instructions from three independent bacterial cultures. After DNase treatment with the Turbo DNA-free™ kit (Ambion), total RNA was purified using acid-phenol solution.

treatment_protocol: For the CosR-knockdown condition, CosR specific PNA (CosR-PNA) was supplemneted into bacterial inoculum to a final concentration of 1.5 uM.

value: wild type

source_name: C. jejuni with CosR specific PNA

value: CosR specific PNA (CosR-PNA)


title: CosR-knockdown replicate 3.

description: Biological replication 3 of 3


title: AML [6247_28nov08]

description: Not Applicable

source_name: AML


title: AML [6245_28nov08]

description: Not Applicable


title: AML [6246_28nov08]

description: Not Applicable


title: AML [6357_20jan09]

description: Not Applicable


title: CosR-knockdown replicate 1.

description: Biological replication 1 of 3


title: RPE_Adult_rep1

city: Harbin

first: Shaomin

last: Peng

address: 246 XueFu Road

country: China

institute: The Second Hospital of Harbin Medical University

description:
differental gene expression of RPE  in adult
Adult

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

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

data_processing: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. NimbleScan software’s implementation of RMA offers quantile normalization and background correction. There are three steps of RMA: Firstly, background subtraction was performed using a local background estimator. Secondly, quantile normalization (Bioinformatics 2003; 19:185) at probe level was done to make the expression distributions the same for all arrays. Last, probe set summarization was performed using Robust Multichip Average (RMA) algorithm as described by Irizarry, et al (Nucleic Acids Res. 2003; 31:e15 and Biostatistics 2003; 4:249).  The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further 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 using the standard enrichment computation method.

source_name: human adult RPE

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

extract_protocol: Equal amounts of RNA were pooled from the 3 independent replicates used for each time point of each group. RNA was extracted using TRIzol (Invitrogen, USA) and the RNeasy kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions. Concentration and quality of RNA was determined using Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and/or Nano drop spectrophotometer (Wilmington, DE, USA). All samples had A (260)/A(280) ratios of the total RNA 2.0, and the ratio of 28S/18S ribosomal RNA bands was more than 1.8.

tag: developmental stage

value: mature adult (40-60 years old)

value: eye

value: retinal pigment epithelium


title: AML [6244_28nov08]

description: Not Applicable

value: Training

value: NPM1 wt


title: AML [6243_21oct08]

description: Not Applicable


title: AML [6242_28nov08]

description: Not Applicable


title: RPE_16W_rep1

description:
differental gene expression of RPE  in 16 weeks gastation
16W

source_name: human fetal RPE

value: fetus (16 weeks of gestation)


title: Udorn1


title: AML [6239_27nov08]

description: Not Applicable

value: NPM1 A


title: AML [6240_27nov08]

description: Not Applicable


title: AML [6237_27nov08]

description: Not Applicable


title: Udorn2

value: middle ear


title: AML [6236_21oct08]

description: Not Applicable


title: AML [5365_21oct08]

description: Not Applicable


title: AML [6241_21oct08]

description: Not Applicable


title: RPE_13W_rep1

description:
differental gene expression of RPE  in 13 weeks gastation
13W

value: fetus (13 weeks of gestation)


title: AML [6238_27nov08]

description: Not Applicable


title: 18°C/1100 µatm pluteus stage replicate 3

city: Santa Barbara

first: Tyler

middle: G

last: Evans

state: California

address: Marine Science Institute

department: Ecology, Evolution and Marine Biology

institute: University of California Santa Barbara

description: Biological replicate 3 of 3 from  18°C/1100 µatm sampled at pluteus stage

hyb_protocol: Amplified and labled RNA whose yield and specific activity exceeded 1.875 µg and 6 pmol, repsectively, were hybridized to each array according to instructions for Agilent's Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol.

scan_protocol: Scanned using an Axon GenePix 4000B microarray scanner, adjusting the PMT gain for optimized visualization of each slide.

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Only genes 2.6 times above background, but not saturated in all samples were analyzed. Different probes targeting the same gene loci (e.g. SPU) were summarized by computing the geometric mean.

organism: Strongylocentrotus purpuratus

source_name: Approx. 8,000 pooled larvae from one 18°C/1100 µatm culture replicate

label_protocol: 200 ng of clean, total RNA from either experimental or reference samples were amplified and labeled with Cy5 or Cy3 fluorescent dyes, respectively, using Agilent's Low-Input Quick Amp Two Color Labeling Kit  (#5190-2306, Agilent Technologies Inc., Santa Clara, CA, USA).

growth_protocol: Ferilized eggs were cultured  under four different seawater pCO2 concentrations and temperatures: (i)13°C/400 µatm pCO2, (ii)13°C/1100 µatm pCO2, (iii)18°C/400 µatm pCO2 (iv)18°C/1100 µatm pCO2. Larval cultures were performed as described in Fangue et al. (2010). A laboratory-based, experimental system for the study of ocean acidification effects on marine invertebrate larvae. Limnology and Oceanography: Methods 8: 441–452.

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

treatment_protocol: pCO2 within each culture was manipulated by bubbling CO2 gas into seawater as described in Fangue et al. (2010). Temperature was controlled by placing culture mesocosms in baths containing seawater at 13°C or 18°C.

tag: Stage

value: Pluteus

tag: culture conditions

source_name: Total RNA pooled from aliquots of total RNA from all experimental samples and labeled with Cyanine-3 (green).

value: Reference


title: 18°C/1100 µatm pluteus stage replicate 1

description: Biological replicate 1 of 3 from  18°C/1100 µatm sampled at pluteus stage


title: 18°C/400 µatm pluteus stage replicate 3

description: Biological replicate 3 of 3 from  18°C/400 µatm sampled at pluteus stage

source_name: Approx. 8,000 pooled larvae from one 18°C/400 µatm culture replicate


title: 18°C/1100 µatm pluteus stage replicate 2

description: Biological replicate 2 of 3 from  18°C/1100 µatm sampled at pluteus stage


title: 18°C/400 µatm pluteus stage replicate 1

description: Biological replicate 1 of 3 from  18°C/400 µatm sampled at pluteus stage


title: 18°C/400 µatm pluteus stage replicate 2

description: Biological replicate 2 of 3 from  18°C/400 µatm sampled at pluteus stage


title: Leaves, antimycin A treated vs untreated

city: Tucson

first: David

middle: M.

last: Rhoads

state: Arizona

address: 1140 East S. Campus Dr.

department: Plant Sciences

institute: University of Arizona

hyb_protocol: Prior to hybridizations, microarrays were rehydrated by exposure to water vapor produced by a 45oC water bath for 5-10 s and then snap dried on a 65oC heating block for 5 s.  This cycle was repeated three times with cooling to about 25oC between each cycle.   DNA was cross-linked to the microarrays by exposure to 180 mJ UV-radiation using a Stratalinker (Stratagene, La Jolla, CA, USA). Microarrays were then washed in 1% SDS for 5 min at about 25oC on a shaker, dipped several times into sterile diethyl pyrocarbonate-treated water, and immediately dipped in and washed with 100% ethanol with shaking at 25oC for 3 min. Finally, microarrays were dried by centrifugation at 1000g for 3 min in slide holders in a table-top centrifuge and used for hybridization. Hybridization mixture (60 uL) consisted of 48 or 96 pmol of dye (which corresponded to about 0.3-0.6 ug of labeled aRNA), 3.6 uL of liquid block (Amersham Biosciences, Piscataway, NJ, USA), 2X SSC, and 0.08% SDS (w/v). The hybridization mixture was incubated in a boiling water bath for 2 min and transferred to ice. A raised cover slip (Fisher Scientific, Pittsburgh, PA, USA) was placed over each microarray and hybridization mixture was applied. The microarray was immediately placed in a hybridization chamber and incubated overnight (8-12 h) at 55oC. After hybridization, microarrays were washed successively for 5 min in 2X SSC and 0.5% (w/v) SDS at 55oC, followed by 0.5X SSC and then 0.05X SSC, both at about 25oC.  The microarray was dried by centrifugation at 1000g for 3 min.

scan_protocol: The microarrays were scanned using a G2565BA Microarray Scanner System (Agilent, Palo Alto, CA, USA).  Quantitative data were extracted from image files of microarrays and further analyzed using GenPix Pro 6.0 software (Molecular Devices, Sunneyvale, CA, USA) and the appropriate GenePix Array List file from the University of Arizona Oligonucleotide Microarray Facility.

data_processing: For analyses of the AA-treated or MFA-treated versus control samples, differences in transcript levels were determined by a two-step mixed model analysis of variance (ANOVA) procedure according to Watkins et al (2003) and Wolfinger et al (2001):[Watkinson JI, Sioson AA, Vasquez-Robinet C, Shukla M, Kumar D, Ellis M, Heath LS, Ramakrishnan N, Chevone B, Watson LT, van Zyl L, Egertsdotter U, Sederoff RR,Grene R (2003) Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine. Plant Physiol 133:1702-1716.; Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushnel P, Afshari C, Paules RS (2001) Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8:625-637.] Data from GenePix software files for each array were log2-transformed.  In the first ANOVA step of the mixed model, these values were scaled and normalized. In the second ANOVA step, these data were used to determine statistically significant differences in gene transcript levels between treated and control samples. The ANOVA steps were performed in SAS version 9 (SAS Institute, Cary, NC). A false discovery rate parameter, the q-value, was calculated using the q-value package provided by Bioconductor to correct for the multi-testing problem and was used to identify significantly differentially expressed genes according to Storey (2003). [Storey JD (2003) The positive false discovery rate: A Bayesian interpretation and the q-value. Ann. Statist 31:2013-2035.]

organism: Arabidopsis thaliana

source_name: leaves, antimycin A treated, 6 hr, dark

label_protocol: Labelled aRNA was produced using Amino Allyl MessageAmp aRNA Amplification Kit according to the protocols of the manufacturer (Ambion, Austin, TX, USA). In brief, 2.0 μg of total RNA was used for first-strand cDNA synthesis. Second-strand cDNA was produced and double-strand cDNA was used in an in vitro transcription reaction to generate amino allyl modified aRNA, 5-10 μg of which was used for coupling to either Cy3 or Cy5 dyes (Amersham Biosciences, Piscataway, NJ, USA). After coupling at 25 oC for 60 min, the reaction was quenched with hydroxylamine. The Cy3- or Cy5-labeled target was purified using an RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA, USA).

growth_protocol: Arabidopsis thaliana Col-0 was grown, with separate plantings for microarray and RNA blot experiments, in Sunshine Mix #1 (Jero, Inc., Waddell, AZ) soil at 21oC during 16 h of light of 100 μmol m-2s-1 and 18oC during the 8 h dark period.  Plants were fertilized with micronutrients and nutrients as described in Scholl et al. (1998) [Scholl, R., Rivero-Lepinckas, L. and Crist, D.. 1998. Growth of plants and preservation of seeds. In: J. Martınez-Zapater and J. Salinas (Eds.), Arabidopsis Protocols, Humana Press, Totowa, NJ, pp. 1–12.] except that NH4H2PO4 was added to the nutrient mix to a final concentration of 1.0 mM.

extract_protocol: Total RNA was isolated from plants (typically 0.5-1 g of rosette tissue) using TRIzol according to the protocol of the manufacturer (Invitrogen, Carlsbad, CA, USA) and treated with TURBO-DNase (TURBO DNA-free kit, Ambion, Austin, TX, USA).  Total RNA was further purified using an RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: For AA treatments, 20 uM antimycin A (AA, Sigma A-8674; Sigma-Aldrich Corp., St. Louis, MO) in 0.01% Tween 20 was sprayed onto the plants. When spraying plants, thorough coverage, as judged by uniform wetting of plant material, was ensured. Initial treatment of plants was at 20 days after germination.

tag: ecotype

tag: growth stage

value: 20 days after germination

tag: growth conditions

value: soil, long-day, 100 umoles/m2/sec light/23oC

value: leaves

value: 20 uM antimycin A in 0.01% Tween 20, 6 hr, dark, 25oC

source_name: leaves, control treated, 6 hr, dark

value: 0.01% Tween 20, 6 hr, dark, 25oC


title: EcfO constitutive vector control

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

description: empty vector control for EcfO constitutive expression experiment

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., using standard protocol as described on their website.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., using standard protocol as described on their website.

data_processing: Raw data (pair files) were 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 by NimbleGen Systems as described on their web site.

organism: Bacteroides fragilis NCTC 9343

source_name: Bacteroides fragilis, ATCC25285, vector control

label_protocol: Labeling was performed by NimbleGen Systems Inc., using standard protocol as described on their website.

growth_protocol: Overnight cultures of the vector control or overexpressing strain were diluted 1/50 into complex media and grown under anaerobic conditions at 37C to mid-logarithmic phase at an A550 of 0.3

extract_protocol: Total RNA was isolated by the hot phenol method and treated as described by Sund et al, 2008, Mol. Microbiol.67:129-142.

tag: synonym

value: Bacteroides fragilis ATCC 25285

tag: transformation construct

value: vector control


title: Leaves, monofluoroacetate treated vs untreated

hyb_protocol: The hybridization mixture was incubated in a boiling water bath for 2 min and transferred to ice. A raised cover slip (Fisher Scientific, Pittsburgh, PA, USA) was placed over each microarray and hybridization mixture was applied. The microarray was immediately placed in a hybridization chamber and incubated overnight (8-12 h) at 55oC. After hybridization, microarrays were washed successively for 5 min in 2X SSC and 0.5% (w/v) SDS at 55oC, followed by 0.5X SSC and then 0.05X SSC, both at about 25oC.  The microarray was dried by centrifugation at 1000g for 3 min.

scan_protocol: The microarrays were scanned using a G2565BA Microarray Scanner System (Agilent, Palo Alto, CA, USA). Quantitative data were extracted from image files of microarrays and further analyzed using GenPix Pro 6.0 software (Molecular Devices, Sunneyvale, CA, USA) and the appropriate GenePix Array List file from the University of Arizona Oligonucleotide Microarray Facility.

data_processing: For analyses of the AA-treated or MFA-treated versus control samples, differences in transcript levels were determined by a two-step mixed model analysis of variance (ANOVA) procedure according to Watkins et al (2003) and Wolfinger et al (2001): [Watkinson JI, Sioson AA, Vasquez-Robinet C, Shukla M, Kumar D, Ellis M, Heath LS, Ramakrishnan N, Chevone B, Watson LT, van Zyl L, Egertsdotter U, Sederoff RR,Grene R (2003) Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine. Plant Physiol 133:1702-1716.; Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushnel P, Afshari C, Paules RS (2001) Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8:625-637.] Data from GenePix software files for each array were log2-transformed.  In the first ANOVA step of the mixed model, these values were scaled and normalized. In the second ANOVA step, these data were used to determine statistically significant differences in gene transcript levels between treated and control samples. The ANOVA steps were performed in SAS version 9 (SAS Institute, Cary, NC). A false discovery rate parameter, the q-value, was calculated using the q-value package provided by Bioconductor to correct for the multi-testing problem and was used to identify significantly differentially expressed genes according to Storey (2003). [Storey JD (2003) The positive false discovery rate: A Bayesian interpretation and the q-value. Ann. Statist 31:2013-2035.]

source_name: leaves, monofluoroacetate treated, 10 hr, dark

label_protocol: Prior to hybridizations, microarrays were rehydrated by exposure to water vapor produced by a 45oC water bath for 5-10 s and then snap dried on a 65oC heating block for 5 s.  This cycle was repeated three times with cooling to about 25oC between each cycle. DNA was cross-linked to the microarrays by exposure to 180 mJ UV-radiation using a Stratalinker (Stratagene, La Jolla, CA, USA). Microarrays were then washed in 1% SDS for 5 min at about 25oC on a shaker, dipped several times into sterile diethyl pyrocarbonate-treated water, and immediately dipped in and washed with 100% ethanol with shaking at 25oC for 3 min. Finally, microarrays were dried by centrifugation at 1000g for 3 min in slide holders in a table-top centrifuge and used for hybridization. Hybridization mixture (60 uL) consisted of 48 or 96 pmol of dye (which corresponded to about 0.3-0.6 μg of labeled aRNA), 3.6 μL of liquid block (Amersham Biosciences, Piscataway, NJ, USA), 2X SSC, and 0.08% SDS (w/v).

growth_protocol: Arabidopsis thaliana Col-0 was grown, with separate plantings for microarray and RNA blot experiments, in Sunshine Mix #1 (Jero, Inc., Waddell, AZ) soil at 21oC during 16 h of light of 100 μmol m-2s-1 and 18oC during the 8 h dark period. Plants were fertilized with micronutrients and nutrients as described in Scholl et al. (1998) [Scholl, R., Rivero-Lepinckas, L. and Crist, D.. 1998. Growth of plants and preservation of seeds. In: J. Martınez-Zapater and J. Salinas (Eds.), Arabidopsis Protocols, Humana Press, Totowa, NJ, pp. 1–12.] except that NH4H2PO4 was added to the nutrient mix to a final concentration of 1.0 mM.

extract_protocol: Total RNA was isolated from plants (typically 0.5-1 g of rosette tissue) using TRIzol according to the protocol of the manufacturer (Invitrogen, Carlsbad, CA, USA) and treated with TURBO-DNase (TURBO DNA-free kit, Ambion, Austin, TX, USA). Total RNA was further purified using an RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA, USA). Labelled aRNA was produced using Amino Allyl MessageAmp aRNA Amplification Kit according to the protocols of the manufacturer (Ambion, Austin, TX, USA). In brief, 2.0 μg of total RNA was used for first-strand cDNA synthesis. Second-strand cDNA was produced and double-strand cDNA was used in an in vitro transcription reaction to generate amino allyl modified aRNA, 5-10 ug of which was used for coupling to either Cy3 or Cy5 dyes (Amersham Biosciences, Piscataway, NJ, USA). After coupling at 25oC for 60 min, the reaction was quenched with hydroxylamine. The Cy3- or Cy5-labeled target was purified using an RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: For MFA treatments, 5 mM monofluoroacetate in 0.01% Tween 20 was sprayed onto the plants. When spraying plants, thorough coverage, as judged by uniform wetting of plant material, was ensured. Initial treatment of plants was at 20 days after germination.

tag: tissue

value: 5mM monofluoroacetate in 0.01% Tween 20, 10 hr, dark, 25oC

source_name: leaves, control treated, 10 hr, dark


title: EcfO constitutive expressed

description: EcfO cloned on pFD340 and constitutively expressed

source_name: Bacteroides fragilis, ATCC25285, expressed from pFD340

value: EcfO expressed on pFD340


title: OSCC methylation 592

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: Tongue

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: GenomeStudio software V2010.3 with GenomeStudio Methylation Version 1.8.5.

source_name: OSCC

label_protocol: Standard Illumina protocol

growth_protocol: not applicable

extract_protocol: Tri-reagent (Sigma)

treatment_protocol: not applicable

tag: gender

value: M

tag: source tissue

value: Tongue

value: Oral cavity squamous cell carcinoma tumor

tag: case


title: 13°C/1100 µatm pluteus stage replicate 2

description: Biological replicate 2 of 3 from  13°C/1100 µatm sampled at pluteus stage

source_name: Approx. 8,000 pooled larvae from one 13°C/1100 µatm culture replicate

tag: sample type


title: 13°C/1100 µatm pluteus stage replicate 3

description: Biological replicate 3 of 3 from  13°C/1100 µatm sampled at pluteus stage


title: Blood methylation JJC2

description: blood

source_name: normal blood sample

value: blood

value: normal blood sample


title: ctrl

city: Norwich

first: Chris

last: den Hengst

state: Norfolk

address: Colney

department: Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

description: Biological replicate 1 of 1.

hyb_protocol: DNA was hybridized to microarrays in an Agilent Technologies microarray chamber by using hybridization buffer (1 M NaCl/50 mM Mes, pH 7/20% formamide/1% Triton X-100) and rotated at 55°C over 40 h. The arrays were then washed with Wash 1 [6× standard saline phosphate/EDTA (0.18 M NaCl/10 mM phosphate, pH 7.4/1 mM EDTA) (SSPE) containing 0.005% N-Lauroyl sarcosine] and Wash 2 (0.06% SSPE/0.18% polyethylene glycol 200), both for 5 min at room temperature.

scan_protocol: For data collection, an Agilent Technologies microarray scanner was used, and results were extracted by using Agilent Technologies Feature Extraction software.

data_processing: Columns containing the positions of probes in the genome sequence, the green median signals and, the red median signals were extracted from the raw data files. Ratios of green median signals to the red median signals were calculated. For the bldC mutant control and the replicates of the wild-type, the signal ratios were read into a data frame in R and scaled to make the mean as well as the standard deviation for each fall within the range of 0 to 1. For each probe, the mean of the two (scaled) bldC ratios was calculated and from it the control ratio was subtracted to arrive at a vector of the differences between the bldC means and the control.  For each of the difference so calculated, a P value was calculated assuming a population mean equal to the mean of all differences and a population standard deviation equal to the standard deviation of all the differences. These P values were adjusted for multiple testing by the method of Benjamini and Hochberg to arrive at adjusted P values. Data were ordered by increasing (adjusted) P values and all probes having an adjusted P value < 5e-3 were manually inspected to determine whether they were a part of a signal peak or not.

organism: Streptomyces coelicolor A3(2)

source_name: BldC ChIP DNA, bldC null mutant cells harvested from log phase in YEME/TSB

label_protocol: Using the Bio-Prime kit (Invitrogen), 800 ng of the total and immunoprecipitated DNA was labelled with Cy5-dCTP and Cy3-dCTP, respectively.

extract_protocol: S. coelicolor was grown in YEME/TSB liquid medium. Wild type was done in duplicate and a single control experiment was done. Formaldehyde was added to cultures at a final concentration of 1% (v/v) and incubation was continued for 30 min.

tag: strain

tag: genotype

value: bldC null mutant

tag: chip antibody

value: anti-BldC antibody (custom made)

source_name: Total DNA control

value: wild-type


title: OSCC methylation 394

description: FOM

value: FOM


title: Normal methylation 173

description: Tongue

source_name: normal oral epithelial tissues

value: normal oral epithelial tissues


title: 13°C/1100 µatm pluteus stage replicate 1

description: Biological replicate 1 of 3 from  13°C/1100 µatm sampled at pluteus stage

value: Pluteus

value: Reference


title: bldc2

description: Biological replicate 2 of 2.

source_name: BldC ChIP DNA, wild-type cells harvested from log phase in YEME/TSB


title: Normal methylation 308

description: Tongue


title: Blood methylation JY8F

description: blood


title: 13°C/400 µatm pluteus stage replicate 3

description: Biological replicate 3 of 3 from  13°C/400 µatm sampled at pluteus stage

source_name: Approx. 8,000 pooled larvae from one 13°C/400 µatm culture replicate

value: 13°C/400 µatm


title: flower Cy5 Leaf Cy3 (590460)

city: Taipei

first: Choun Sea

last: Lin

address: 128 Academia Road, Section 2

department: Agriculture Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

description: Analysis used leaves from Oncidium Gower Ramsey were maintained in the greenhouse RNA as control samples for comparison to the experimental samples taken  flowers  from Oncidium Gower Ramsey

hyb_protocol: cDNA hybridization and washing procedures were performed according to the 3DNA Expression Array Detection kit manufacturer's instructions.

scan_protocol: Arrays scanned using a Axon genepix 4000B scanner and images were analyzed using GenePix Pro Software

data_processing: Quality flagging was performed on the microarray scans using GenePix Pro. Data files were imported into GeneSpring software for further analyses.

organism: Oncidium hybrid cultivar

source_name: flowers

label_protocol: The total RNA of leaves and flowers (25 μg) was used for cDNA synthesis and labeling with either Cy3 or Cy5 dye, using the 3DNA Expression Array Detection kit for microarrays (Array 50, version 2, Genisphere, Hatfield, PA).

growth_protocol: Flowering Onc. GR were obtained from a local Gower (Yung Hsin Orchid Nursery, Taichung, Taiwan). These orchids were maintained in the greenhouse at Academia Sinica, Taipei, Taiwan, and a voucher specimen was deposited at the National Museum of Natural Science, Taichung, Taiwan.

extract_protocol: Total RNA and poly(A)+ mRNA were isolated using the Trizol reagent (Invitrogen, Carlsbed, CA) and the Oligotex Midi mRNA kit (Qiagen, Venlo, The Netherlands), respectively, according to the manufacturer’s instructions. Total RNA (5 µg) extracted from different tissues was subjected to RT-PCR. First-strand cDNAs were synthesized using M-MLV reverse transcriptase (RNase H Minus, Point mutant; Promega, Madison, WI) and a poly (dT) primer. Each gene was amplified for 25 PCR cycles using primers specific for each gene. Onc. GR ubiquitin was used as an internal control. The primers used are shown in Table 1.

value: flower

source_name: leaves

value: leaf


title: bldc1

description: Biological replicate 1 of 2.


title: OSCC methylation 575

description: Alveolar

value: Alveolar


title: 13°C/400 µatm pluteus stage replicate 2

description: Biological replicate 2 of 3 from  13°C/400 µatm sampled at pluteus stage

source_name: Total RNA pooled from aliquots of total RNA from all experimental samples and labeled with Cyanine-3 (green).


title: OSCC methylation 537

description: Buccal

value: Buccal


title: flower Cy3 Leaf Cy5 (495465)


title: flower Cy3 Leaf Cy5 (520545)


title: flower Cy5 Leaf Cy3 (630450)


title: 13°C/400 µatm pluteus stage replicate 1

description: Biological replicate 1 of 3 from 13°C/400 µatm sampled at pluteus stage


title: OSCC methylation 449

description: Tongue

value: M


title: OSCC methylation 201

description: FOM


title: flower Cy3 Leaf Cy5 (49485)


title: OSCC methylation 193

description: Buccal


title: Pluteus Culture 1200µatm CO2 Replicate 4

description:
Biological replicate 4 of 4 at 1200µatm at pluteus stage
Sample 24

hyb_protocol: Amplified and labeled RNA whose yield and specific activity exceeded 1.875 µg and 6 pmol, repsectively, were hybridized to each array according to instructions for Agilent's Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol.

source_name: Approx. 60,000 pooled larvae from one 1200µatm CO2 culture replicate

growth_protocol: Ferilized eggs were cultured  under three different seawater CO2 concentrations 400, 800, 1200 µatm as described in Fangue et al. (2010). A laboratory-based, experimental system for the study of ocean acidification effects on marine invertebrate larvae. Limnology and Oceanography: Methods 8: 441–452.

treatment_protocol: pCO2 within each culture was manipulated by bubbling CO2 gas into seawater as described in Fangue et al. (2010).

value: Approx. 60,000 pooled larvae

value: Pluteui

tag: seawater co2 concentrations

value: pooled reference


title: Pluteus Culture 1200µatm CO2 Replicate 3

description:
Biological replicate 3 of 4 at 1200µatm at pluteus stage
Sample 23

tag: developmental stage


title: OSCC methylation 169

description: FOM

value: F

value: Oral cavity squamous cell carcinoma tumor


title: Pluteus Culture 1200µatm CO2 Replicate 2

description:
Biological replicate 2 of 4 at 1200µatm at pluteus stage
Sample 22


title: OSCC methylation 288

description: Tongue

value: Tongue


title: OSCC methylation 562

description: Tongue


title: Pluteus Culture 1200µatm CO2 Replicate 1

description:
Biological replicate 1 of 4 at 1200µatm at pluteus stage
Sample 21


title: wild-type vs. flb4-deleted mutant rep12

city: Kaiserslautern

first: Karsten

last: Andresen

address: Erwin-Schroedinger-Str. 56

institute: IBWF

description:
biological replicate 3
flb4-wt-6.txt
flb4-wt-rep12

hyb_protocol: Following the manufacturer’s instructions supplied with Aglilent platform.

scan_protocol: Agilent Technologies Scanner System (Scanner Model G2505B) was used with Agilent Scan Control Software Version A.7.0.1

data_processing: Preliminary processing of data was made using the Agilent Feature Extraction Software (9.5.1.1). Prior to normalization all data related to the expression of Oryza sativa genes have been removed. Data normalisation and statistical analyses were performed using Bioconductor R package Limma. Raw signals were background corrected by subtracting local spot background. Two normalization methods were applied: first within arrays using the global loess method and second between the arrays using the Aquantile method. There are two technical replicates of each biological sample (derived from one raw data file indicated in 'Description' and available as Series Supplementary file). The output files from Feature Extraction, where each probe appears twice in the column ProbeName, were filtered with a script that sorted the first appearance of a probe in the column ProbeName to the first replicate and the second appearance to the second replicate.

organism: Pyricularia oryzae

label_protocol: RNA was labelled with Cy3 and Cy5 dyes using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Cat. No. 5184-3523) following the manufacturer’s instructions.

growth_protocol: 11 day old CM (Talbot et al., 1993) agar cultures

extract_protocol: RNA was obtained from the aerial mycelium by grinding in liquid nitrogen and extraction using the Qiagen plant RNA extraction kit.

treatment_protocol: Aerial mycelium was obtained by shaving the surface of 11 day old CM agar cultures of the respective strains with a sterile scalpel.

tag: strain background

tag: genotype/variation

value: flb4 mutant

tag: age

value: 11 days old CM agar cultures

value: Aerial mycelium

source_name: wt

value: wild type


title: OSCC methylation 530

description: FOM

value: FOM


title: OSCC methylation 180

description: Tongue


title: OSCC methylation 364

description: Alveolar


title: wild-type vs. flb4-deleted mutant rep10

description:
biological replicate 3
flb4-wt-5.txt
flb4-wt-rep10


title: OSCC methylation 281

description: Tongue


title: Pluteus Culture 800µatm CO2 Replicate 4

description:
Biological replicate 4 of 4 at 800µatm at pluteus stage
Sample 20

source_name: Approx. 60,000 pooled larvae from one 800µatm CO2 culture replicate


title: flower Cy5 Leaf Cy3 (560450)


title: wild-type vs. flb4-deleted mutant rep11

description:
biological replicate 3
flb4-wt-6.txt
flb4-wt-rep11


title: wild-type vs. flb4-deleted mutant rep9

description:
biological replicate 3
flb4-wt-5.txt
flb4-wt-rep9


title: wild-type vs. flb4-deleted mutant rep8

description:
biological replicate 2
flb4-wt-4.txt
flb4-wt-rep8


title: Pluteus Culture 800µatm CO2 Replicate 3

description:
Biological replicate 3 of 4 at 800µatm at pluteus stage
Sample 19


title: Pluteus Culture 800µatm CO2 Replicate 2

description:
Biological replicate 2 of 4 at 800µatm at pluteus stage
Sample 18


title: OSCC methylation 234

description: Tongue


title: Pluteus Culture 800µatm CO2 Replicate 1

description:
Biological replicate 1 of 4 at 800µatm at pluteus stage
Sample 17


title: OSCC methylation 489

description: FOM


title: OSCC methylation 298

description: Tongue


title: Pluteus Culture 400µatm CO2 Replicate 3

description:
Biological replicate 3 of 4 at 400µatm at pluteus stage
Sample 15

source_name: Approx. 60,000 pooled larvae from one 400µatm CO2 culture replicate


title: Pluteus Culture 400µatm CO2 Replicate 2

description:
Biological replicate 2 of 4 at 400µatm at pluteus stage
Sample 14


title: wild-type vs. flb4-deleted mutant rep5

description:
biological replicate 2
flb4-wt-3.txt
flb4-wt-rep5


title: wild-type vs. flb4-deleted mutant rep4

description:
biological replicate 1
flb4-wt-2.txt
flb4-wt-rep4


title: wild-type vs. flb4-deleted mutant rep6

description:
biological replicate 2
flb4-wt-3.txt
flb4-wt-rep6


title: wild-type vs. flb4-deleted mutant rep7

description:
biological replicate 2
flb4-wt-4.txt
flb4-wt-rep7


title: OSCC methylation 37

description: FOM


title: OSCC methylation 331

description: FOM


title: OSCC methylation 513

description: Tongue


title: wild-type vs. flb4-deleted mutant rep3

description:
biological replicate 1
flb4-wt-2.txt
flb4-wt-rep3


title: Gastrula Culture 1200µatm CO2 Replicate 4

description:
Biological replicate 4 of 4 at 1200µatm at gastrula stage
Sample 12

value: Gastrulae


title: wild-type vs. flb4-deleted mutant rep2

description:
biological replicate 1
flb4-wt-1.txt
flb4-wt-rep2


title: Gastrula Culture 1200µatm CO2 Replicate 3

description:
Biological replicate 3 of 4 at 1200µatm at gastrula stage
Sample 11


title: wild-type vs. flb4-deleted mutant rep1

description:
biological replicate 1
flb4-wt-1.txt
flb4-wt-rep1


title: Pluteus Culture 400µatm CO2 Replicate 4

description:
Biological replicate 4 of 4 at 400µatm at pluteus stage
Sample 16


title: OSCC methylation 600

description: Tongue


title: Gastrula Culture 1200µatm CO2 Replicate 1

description:
Biological replicate 1 of 4 at 1200µatm at gastrula stage
Sample 9


title: Gastrula Culture 1200µatm CO2 Replicate 2

description:
Biological replicate 2 of 4 at 1200µatm at gastrula stage
Sample 10


title: wild-type vs. flb3-deleted mutant rep11

description:
biological replicate 3
flb3-wt-6.txt
flb3-wt-rep11

value: flb3 mutant


title: Gastrula Culture 800µatm CO2 Replicate 4

description:
Biological replicate 4 of 4 at 800µatm at gastrula stage
Sample 8


title: OSCC methylation 392

description: Tongue


title: OSCC methylation 353

description: Tongue


title: wild-type vs. flb3-deleted mutant rep12

description:
biological replicate 3
flb3-wt-6.txt
flb3-wt-rep12


title: Gastrula Culture 800µatm CO2 Replicate 3

description:
Biological replicate 3 of 4 at 800µatm at gastrula stage
Sample 7


title: Gastrula Culture 800µatm CO2 Replicate 2

description:
Biological replicate 2 of 4 at 800µatm at gastrula stage
Sample 6


title: OSCC methylation 478

description: Tongue


title: wild-type vs. flb3-deleted mutant rep7

description:
biological replicate 2
flb3-wt-4.txt
flb3-wt-rep7


title: wild-type vs. flb3-deleted mutant rep9

description:
biological replicate 3
flb3-wt-5.txt
flb3-wt-rep9


title: OSCC methylation 481

description: Tongue


title: Pluteus Culture 400µatm CO2 Replicate 1

description:
Biological replicate 1 of 4 at 400µatm at pluteus stage
Sample 13


title: wild-type vs. flb3-deleted mutant rep6

description:
biological replicate 2
flb3-wt-3.txt
flb3-wt-rep6


title: OSCC methylation 229

description: FOM


title: Gastrula Culture 400µatm CO2 Replicate 4

description:
Biological replicate 4 of 4 at 400µatm at gastrula stage
Sample 4


title: wild-type vs. flb3-deleted mutant rep8

description:
biological replicate 2
flb3-wt-4.txt
flb3-wt-rep8


title: OSCC methylation 385

description: Tongue


title: Gastrula Culture 800µatm CO2 Replicate 1

description:
Biological replicate 1 of 4 at 800µatm at gastrula stage
Sample 5


title: OSCC methylation 325

description: Tongue


title: OSCC methylation 238

description: Tongue


title: Gastrula Culture 400µatm CO2 Replicate 3

description:
Biological replicate 3 of 4 at 400µatm at gastrula stage
Sample 3


title: OSCC methylation 327

description: Tongue


title: OSCC methylation 266

description: Tongue


title: Gastrula Culture 400µatm CO2 Replicate 1

description:
Biological replicate 1 of 4 at 400µatm at gastrula stage
Sample 1


title: wild-type vs. flb3-deleted mutant rep5

description:
biological replicate 2
flb3-wt-3.txt
flb3-wt-rep5


title: OSCC methylation 258

description: Tongue


title: wild-type vs. flb3-deleted mutant rep2

description:
biological replicate 1
flb3-wt-1.txt
flb3-wt-rep2


title: wild-type vs. flb3-deleted mutant rep3

description:
biological replicate 1
flb3-wt-2.txt
flb3-wt-rep3


title: OSCC methylation 391

description: Tongue


title: wild-type vs. flb3-deleted mutant rep1

description:
biological replicate 1
flb3-wt-1.txt
flb3-wt-rep1


title: wild-type vs. flb3-deleted mutant rep10

description:
biological replicate 3
flb3-wt-5.txt
flb3-wt-rep10


title: wild-type vs. flb3-deleted mutant rep4

description:
biological replicate 1
flb3-wt-2.txt
flb3-wt-rep4


title: C.elegans fed with CNCM I-4317 10 days rep2

status: Public on Dec 31 2012

city: Montevideo

first: Tamara

last: Fernandez-Calero

state: Montevideo

address: Mataojo 2020

department: Bioinfomatics Unit

country: Uruguay

institute: Institut Pasteur de Montevideo

description: Gene expression data from C.elegans fed with CNCM I-4317 for 10 days

hyb_protocol: Hybridization was performed as described by the manufacturer (Affymetrix, SantaClara, CA). The complementary RNA hybridization cocktail was incubated overnight at 45C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450, according to the Affymetrix-recommended protocol.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA)

data_processing: Data analysis was accomplished in “R” (R Foundation for Statistical Computing, Vienna, Austria; http://www.R-project.org) mainly through packages in the “Bioconductor” suite. Normalization was performed using rma (robust multi-array average expression measure) in “affy”.

organism: Caenorhabditis elegans

label_protocol: Total RNA (300 ng per sample) was labeled using the Affymetrix GeneChip 3´GeneChip®3’ IVT Express Kit protocol.

growth_protocol: Synchronized populations were obtained from embryos isolated from gravid adults in the different feeding conditions. After feeding period (3 or 10 days) of worms were collected with M9 buffer, washed three times and collected in eppendorf tubes for worm disruption by sonication (3 pulses at 10 W, 20 s/pulse).

extract_protocol: Total RNA isolation was performed with RNAasy Kit (Qiagen, Barcelona, Spain).

tag: diet

value: Lactobacillus rhamnosus CNCM I-4317

tag: time

value: 10 days


title: C.elegans fed with CNCM I-3690 10 days rep2

description: Gene expression data from C.elegans fed with CNCM I-3690 for 10 days

value: Lactobacillus rhamnosus CNCM I-3690


title: Gastrula Culture 400µatm CO2 Replicate 2

description:
Biological replicate 2 of 4 at 400µatm at gastrula stage
Sample 2


title: C.elegans fed with CNCM I-4317 10 days rep1

source_name: C.elegans fed with CNCM I-4317 for 10 days


title: C.elegans fed with E.coli OP50 10 days rep2

description: Gene expression data from C.elegans fed with E.coli OP50 for 10 days

value: E. coli OP50 (control condition)


title: C.elegans fed with CNCM I-3690 10 days rep3

source_name: C.elegans fed with CNCM I-3690 for 10 days


title: OSCC methylation 43

description: Tongue

source_name: OSCC

value: M


title: C.elegans fed with CNCM I-4317 3 days rep1

description: Gene expression data from C.elegans fed with CNCM I-4317 for 3 days

value: 3 days


title: C.elegans fed with CNCM I-4317 3 days rep2

source_name: C.elegans fed with CNCM I-4317 for 3 days


title: C.elegans fed with CNCM I-3690 3 days rep1

description: Gene expression data from C.elegans fed with CNCM I-3690 for 3 days


title: C.elegans fed with E.coli OP50 10 days rep3

source_name: C.elegans fed with E.coli OP50 for 10 days


title: C.elegans fed with CNCM I-3690 3 days rep2

source_name: C.elegans fed with CNCM I-3690 for 3 days


title: C.elegans fed with CNCM I-3690 10 days rep1


title: OSCC methylation 166

description: Tongue


title: C.elegans fed with CNCM I-4317 3 days rep3


title: C.elegans fed with E.coli OP50 10 days rep1


title: OSCC methylation 578

description: Tongue


title: OSCC methylation 347

description: Tongue


title: C.elegans fed with E.coli OP50 3 days rep3

description: Gene expression data from C.elegans fed with E.coli OP50 for 3 days


title: OSCC methylation 388

description: Tongue