title: miR-212

city: Jupiter

first: Paul

middle: J.

last: Kenny

state: FL

address: 130 Scripps Way

department: Molecular Therapeutics

institute: The Scripps Research Institute - Florida

description: Gene expression from miR-212 transfected cells

hyb_protocol: cDNA was hybridized to an Affymetrix microarray overnight in the Affymetrix 640 hybridization oven with a speed of 60 rpm for 16 h.

scan_protocol: GeneChip arrays were scanned using a GeneChip Scanner 3000 (Affymetrix)

data_processing:
The probeset intensities were quantified using the GeneChip Operating Software and analyzed with GeneChip Robust Multichip Average (GC-RMA) normalization using Array Assist Software (Stratagene, La Jolla, CA).

DATA FILTERING: Only those probesets in the pMIF-treated cells with an intensity greater or equal to 100 were included in further analyses. The complete, unfiltered set of signal intensity data for Samples miR-212 and pMIF, including miR-212/pMIF ratios, are in the supplementary file of the Series GSE21901 record.  Probes excluded from analysis (pMIF intensity <100) are indicated in the supplementary file by a no in the far-right column, 'Passed data filtering and included in analysis: no/yes'. Probes that were included in the analyses (pMIF intensity >100) are indicated in the supplementary file by a yes in the 'Passed data filtering and included in analysis: no/yes' column.

source_name: HEK 293 cells,  transfected with a vector to overexpress miR-212

label_protocol: Double-stranded cDNA was prepared from 1 μg of total RNA using the Affymetrix cDNA synthesis kit and was then in vitro-transcribed using an IVT labeling kit (Affymetrix), with the cRNA product purified using a GeneChip Sample Cleanup Module (Affymetrix). Biotin-labeled cRNA (20 μg) was fragmented and hybridized toarray.

growth_protocol: HEK 293 cells were grown according to standard protocols

extract_protocol: Total RNA was extracted from HEK 293 cells using RNeasy (Qiagen) kit according to manufacturer's instructions. Samples were quantified using the NanoDrop ND-1000 spectrophotometer

treatment_protocol: HEK 293 cells were transfected with an empty vector (pMIF cells) or a vector to overexpress the immature miR-212 transcript (miR-212 cells)

tag: cell line

value: HEK 293 cells

tag: protocol

value: miR-212 overexpression


title: WT3

status: Public on Jul 07 2010

type: RNA

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

country: USA

institute: Beth Israel Deaconess Medical Center

description: wild type no3

hyb_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome 430 2.0 arrays.

scan_protocol: Affymetrix Scanner/protocol

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

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Murine Lung

label_protocol: For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer's instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.

extract_protocol: Total RNA was isolated using the RNAeasy kit (QIAGEN) following the manufacturer's instructions.

tag: genotype/variation

value: wiltype mouse

tag: tissue type

value: murine neonatal lung tissue


title: pMIF

status: Public on Jul 08 2010

description: Gene expression from pMIF transfected cells

organism: Homo sapiens

source_name: HEK 293 cells,  transfected with an empty vector

value: control


title: Leukemia, Immunophenotype B/T biphenotypic acute leukemia (B/T BAL)

city: Frankfurt/Main

first: Rolf

last: Marschalek

address: Max-von-Laue-Str. 9

department: Inst Pharm Biology

country: Germany

institute: Goethe University

description: Gene expression data from leukemic cells with a B/T BAL immmunophenotype

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip MG-430_2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in a GeneChip Scanner 3000 (G7 update)

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: hematopoietic stem/precursor cells transduced with AF4-MLL  that developed leukemia

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix standard protocol (2 µg RNA)

growth_protocol: Bone marrow cells were isolated after several month from moribund mice that developed leukemia

extract_protocol: RNA was extracted using the Rneasy mini kit (QIAGEN)

treatment_protocol: Cells were not sorted rather than anylzed by FACS fro their immunophenotype; 3 different immunophenotypes were revealed

tag: disease state

value: leukemia

tag: cell type

value: leukemic cells (isolated from bone marrow of diseased mouse)

tag: immunophenotype


title: shSep15 - repeat 3 - mAdbID:101323

city: Towson

first: Petra

last: Tsuji

state: MD

address: 8000 York Rd

department: Biological Sciences

institute: Towson University

description:
targeted down-regulation
The pU6-m3 vector used for generating shRNA targets was constructed as described elsewhere (11, 12). To knockdown Sep15 expression, 19-nt sequence 5’-acagaagagttccatttaa-3’ was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3 as previously described (11).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101323

hyb_protocol: Affymetrix Hybridization Protocol Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 430.

scan_protocol: Affymetrix Scanning Protocol The Scanner 3000 was used to scan the microarrays.

data_processing:
Affymetrix RMA Data Processing
Calculation Method: Expression summary values were calculated using the Bioconductor implemented version of RMA (Robust Multichip Average).

label_protocol:
Affymetrix Labeling Protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Trizol Extraction Protocol
Total RNA was extracted from cells using TRIzol® Reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

tag: strain

value: BALB/c

tag: tissue

value: colon

value: murine colon carcinoma

tag: transfection

value: pU6-m3 vector used for generating shRNA targets. To knockdown Sep15 expression, 19-nt sequence 5’-acagaagagttccatttaa-3’ was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3.


title: Leukemia, Immunphenotype proB ALL

description: Gene expression data from leukemic cells with a proB ALL immmunophenotype

value: proB ALL


title: White adipose tissue in wild-type mice (rep2)

city: Beijing

first: Yinxin

last: Zhang

address: Room C131, School of Medicine, Tsinghua University

department: School of Life Sciences

country: China

institute: Tsinghua University

description: Hybridization and data collection were carried out by the Microarray facility at the Institute of Molecular and Cell Biology in Singapore.

hyb_protocol: Affymetrix EukGE-WS2v4 Hybridization

scan_protocol: HP Affymetrix Gene Array Scanner

data_processing: Affymetrix GeneChip Operating Software (GCOS) version 1.4

source_name: gonadal WAT of five wild-type mice

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

extract_protocol: TRIzol reagent (Invitrogen, USA)

value: WAT

value: wild-type

tag: gender

value: male

tag: age

value: 3 month


title: Leukemia, Immunophenotype mixed lineage leukemia (MLL)

description: Gene expression data from leukemic cells with an MLL immmunophenotype

source_name: hematopoietic stem/precursor cells transduced with AF4-MLL and MLL-AF4 that developed leukemia

value: mixed lineage leukemia (MLL)


title: WT2

description: wild type no2


title: KN2

description: Carm1 knockout 2

source_name: CRAM1 KN mice (lungs)

value: CRAM1 knockout

value: lung, when pups are at embryo stage 18.5 days


title: Control - repeat 3 - mAdbID:101317

description:
The empty pU6-m3 vector was transfected into the cells as described elsewhere (11, 12).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101317

source_name: Control

value: empty pU6-m3 vector


title: KN1

description: Carm1 knockout 1


title: normal bone marrow

description: control

source_name: normal bone marrow cells (control)

value: bone marrow cells

value: normal


title: White adipose tissue in Fsp27 knockout mice (rep1)

source_name: gonadal WAT of five Fsp27 knockout mice

value: Fsp27 knockout


title: White adipose tissue in wild-type mice (rep1)


title: shSep15 - repeat 1 - mAdbID:101321

description:
targeted down-regulation
The pU6-m3 vector used for generating shRNA targets was constructed as described elsewhere (11, 12). To knockdown Sep15 expression, 19-nt sequence 5’-acagaagagttccatttaa-3’ was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3 as previously described (11).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101321


title: AG40_5F7-5F31-138868

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: According to manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

extract_protocol: Total RNA extracted using the nucleospin RNA II kit from Macherey-Nagel.


title: shSep15 - repeat 2 - mAdbID:101322

description:
targeted down-regulation
The pU6-m3 vector used for generating shRNA targets was constructed as described elsewhere (11, 12). To knockdown Sep15 expression, 19-nt sequence 5’-acagaagagttccatttaa-3’ was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3 as previously described (11).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101322


title: WT1

description: wild type no1

value: wiltype mouse

value: murine neonatal lung tissue


title: AG39_5F31-5F7-138867

label_protocol: According to manufacturer's instructions.


title: embryo at 9th week, biological rep3

city: Wuhan

first: Wenxin

last: Li

email: liwxlab@whu.edu.cn, guomx@whu.edu.cn, jinyangc13@126.com, sparkler830305@hotmail.com

state: Hubei

address: Wuhan University, Luojia Hill,Wuhan 430072,China

department: College of Life Science

institute: Wuhan Univeristy

description: Gene expression data from embryos at 9th week after fertilization.

hyb_protocol: Following fragmentation, 10~15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Genome U133 Plus 2.0 Array in Genechip hybridization oven 640. GeneChips were washed and stained in the Affymetrix Genechip fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArrayTM scanner 3000.

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250 after removing the highest 2% and lowest 2% signals.

source_name: Human embryos at 9th week after fertilization

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5~10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

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

treatment_protocol: Morphologically normal embryos were selected and staged according to the Carnegie classification and the Chinese embryonic developmental characteristics. Selected embryos were dechorionated with PBS and stored directly in liquid nitrogen or homogenized using Trizol solution(Invitrogen) at -80℃.

value: dechorionated embryo

tag: development stage

value: 9th week after fertilization


title: Control - repeat 2 - mAdbID:101316

description:
The empty pU6-m3 vector was transfected into the cells as described elsewhere (11, 12).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101316

value: BALB/c

value: colon

value: murine colon carcinoma


title: AG42_5M21-5F31-138870


title: AG41_5F31-5M21-138869


title: Control - repeat 1 - mAdbID:101315

description:
The empty pU6-m3 vector was transfected into the cells as described elsewhere (11, 12).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101315


title: WT3_d14

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description: pulmonary CD11c+ cells from wildtype mouse 3 at day 14 post infection

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix scanner 7G.

data_processing: The data were imported into Genespring using RMA preprocessing for analysis.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 6 wildtype and 6 IFNAR-/- mice were Pneumocystis infeced via intratracheal instillation of 10e7 PC nuclei. 3 mice from each group were harvested at day 7 and at day 14 post infection and lungs processed as described below

extract_protocol: Rneasy (Qiagen)  extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Lungs of infected animals were excised, cut into small pieces , placed into RPMI containing 50U/ml Collagenase IV and 1U/ml DNase and incubated at 37oC for 1 hour. The obtained single cell suspesnion was filtered and incubated in the presence of beads-labeled anti-CD11c antibody and further processed according to the manufacturer's  (Miltenyi) protocol. Purity of isolated cells were >90%. contaminating cells consisted of  < 5% lymphocytes and soem unidentified cells

value: lung

value: primary pulmonary CD11c+ cells


title: WT3_d7

description: pulmonary CD11c+ cells from wildtype mouse 3 at day 7 post infection


title: embryo at 9th week, biological rep2


title: WT2_d14

description: pulmonary CD11c+ cells from wildtype mouse 2 at day 14 post infection


title: WT1_d14

description: pulmonary CD11c+ cells from wildtype mouse 1 at day 14 post infection


title: embryo at 8th week, biological rep1

description: Gene expression data from embryos at 8th week after fertilization.

source_name: Human embryos at 8th week after fertilization

value: 8th week after fertilization


title: embryo at 8th week, biological rep2


title: embryo at 8th week, biological rep3


title: embryo at 7th week, biological rep1

description: Gene expression data from embryos at 7th week after fertilization.

source_name: Human embryos at 7th week after fertilization

value: 7th week after fertilization


title: IFN3_d14

description: pulmonary CD11c+ cells from IFNAR-/- mouse 3 at day 14 post infection


title: embryo at 6th week, biological rep3

description: Gene expression data from embryos at 6th week after fertilization.

source_name: Human embryos at 6th week after fertilization

value: 6th week after fertilization


title: embryo at 7th week, biological rep3


title: IFN2_d14

description: pulmonary CD11c+ cells from IFNAR-/- mouse 2 at day 14 post infection


title: embryo at 9th week, biological rep1


title: WT2_d7

description: pulmonary CD11c+ cells from wildtype mouse 2 at day 7 post infection


title: IFN1_d14

description: pulmonary CD11c+ cells from IFNAR-/- mouse 1 at day 14 post infection


title: embryo at 6th week, biological rep1


title: embryo at 5th week, biological rep1

description: Gene expression data from embryos at 5th week after fertilization.

source_name: Human embryos at 5th week after fertilization

value: 5th week after fertilization


title: IFN2_d7

description: pulmonary CD11c+ cells from IFNAR-/- mouse 2 at day 7 post infection


title: embryo at 7th week, biological rep2


title: embryo at 5th week, biological rep2


title: embryo at 5th week, biological rep3


title: IFN1_d7

description: pulmonary CD11c+ cells from IFNAR-/- mouse 1 at day 7 post infection


title: embryo at 6th week, biological rep2


title: WT1_d7

description: pulmonary CD11c+ cells from wildtype mouse 1 at day 7 post infection


title: IFN3_d7

description: pulmonary CD11c+ cells from IFNAR-/- mouse 3 at day 7 post infection


title: embryo at 4th week, biological rep3

description: Gene expression data from embryos at 4th week after fertilization.

source_name: Human embryos at 4th week after fertilization

value: 4th week after fertilization


title: embryo at 4th week, biological rep2


title: embryo at 4th week, biological rep1


title: 171h vs. 195h  Sample_3256

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: RNA sampled during four 10-day spontaneous wheat sourdough fermentations with daily back-slopping carried out in the laboratory.

hyb_protocol: Hybridization mixtures were prepared using 60 pmol labeled aRNA in 210 µl hybridization buffer (GE Healthcare) containing 50% (vol/vol) formamide (Sigma-Aldrich). The hybridization mixtures were denatured at 96°C for 3 min, put on ice for at least 5 min, hold at 42°C for 5 min, and subsequently microcentrifuged (16,060 g for 5 min). Hybridizations were performed on the automated hybridization station HS 4800 Pro (Tecan, Mannedorf, Switzerland) at 32°C for 16 h. Post-hybridization washing (automated) was performed as follows: 20 s at 32°C, 20 s at 27°C, and 30 s at 23°C in 1 x SSC with 0.2% (wt/vol) SDS; soaking 30 s at 23°C; 30 s at 23°C in 0.1 x SSC with 0.2% (wt/vol) SDS; soaking 30 s at 23°C; 30 s at 23°C in 0.1 x SSC with 0.2% (wt/vol) SDS; soaking 30 s at 23°C; and 30 s in 0.1 x SSC at 23°C. Slides were dried using isopropanol and air.

scan_protocol: Slides were scanned using the Agilent scanner (Agilent) at 10 micron and images were analysed using ArrayVision v7 (GE Healthcare).

data_processing: We apply a background correction, i.e. we subtract the local background for the local foreground intensities. We compute the base 2 log-ratio (ratio of Cy5/Cy3) for each probe and average the log-ratios over the 4 replicates on the array.

organism:
Leuconostoc mesenteroides
Oenococcus oeni
Pediococcus acidilactici
Pediococcus pentosaceus
Staphylococcus aureus
Streptococcus thermophilus
Enterococcus faecalis
Enterococcus faecium
Enterococcus hirae
Lactococcus lactis
Lactobacillus acidophilus
Levilactobacillus brevis
Lentilactobacillus buchneri
Lacticaseibacillus casei
Weissella confusa
Lactobacillus delbrueckii
Lactobacillus helveticus
Lentilactobacillus hilgardii
Lactiplantibacillus pentosus
Lactiplantibacillus plantarum
Lactobacillus gasseri
Lacticaseibacillus paracasei
Limosilactobacillus reuteri
Latilactobacillus sakei
Companilactobacillus alimentarius
Lactobacillus amylovorus
Companilactobacillus farciminis
Limosilactobacillus fermentum
Fructilactobacillus fructivorans
Fructilactobacillus sanfranciscensis
Bifidobacterium
Brevibacterium linens
Latilactobacillus curvatus
Lactobacillus johnsonii
Leuconostoc citreum
Leuconostoc pseudomesenteroides
Limosilactobacillus pontis
Enterococcus casseliflavus
Mammaliicoccus lentus
Limosilactobacillus panis
Lacticaseibacillus rhamnosus
Lactobacillus crispatus
Enterococcus mundtii
Lactiplantibacillus paraplantarum
Companilactobacillus paralimentarius
Limosilactobacillus frumenti
Lentilactobacillus parabuchneri
Companilactobacillus mindensis
Furfurilactobacillus rossiae

label_protocol: RNA was linearly amplified using Genisphere SensAmp kit (Genisphere, Hatfield, Pennsylvania, USA) using 200 ng of total RNA. The protocol was followed according to manufacturer's instructions. The amplified RNA (aRNA) was purified using the RNeasy Mini Kit (Qiagen), and the purified aRNA was Cy5 labeled by a reverse transcription reaction as earlier described by Puskas LG, Zvara A, Hackler L, Van Hummelen P: RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 2002, 32(6):1330-1340.

extract_protocol: Samples taken after 3 h of fermentation were immediately treated with RNAprotect (Qiagen, Hilden, Germany). Therefore, 10 g of sourdough was mixed with 40 ml of RNAprotect that was 2:1 diluted with 1 x phosphate-buffered saline (Invitrogen, Carslbad, USA). This mixture was kept at room temperature for 5 min, followed by centrifugation (1,000 g for 5 min). The supernatant was centrifuged for a second time (5,000 g for 15 min) and the resulting pellet was resuspended in 200 µl TE buffer (30 mM Tris-HCl, 1 mM EDTA, pH 8.0), containing 5 U µl-1 of mutanolysin (Sigma-Aldrich) and 50 µg µl-1 of lysozyme (Sigma-Aldrich). This mixture was incubated in a shaking water bath at 37°C for 1 h. According to the RNeasy Mini Kit protocol (Qiagen), 700 µl of RLT buffer plus ß-mercaptoethanol (10 µl ml-1) was added to the lysate, the solution was mixed, and transferred to a tube containing approximately 50 mg of acid-washed beads (Sigma-Aldrich). After vortexing for 5 min and microcentrifugation (16,060 g for 10 s), 850 µl of supernatant was added to 590 µl of 80% (vol/vol) ethanol, and this mixture was applied on the RNeasy Mini column (Qiagen). Manufacturer’s standard instructions were followed from that point on. RNA quality was checked by both measuring the 260/230 and 260/280 nm ratios, using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, USA) and capillary electrophoresis using a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, USA).

tag: sampling time

label_protocol: RNA was linearly amplified using Genisphere's SensAmp kit (Genisphere, Hatfield, Pennsylvania, USA) using 200 ng of total RNA. The protocol was followed according to manufacturer's instructions. The amplified RNA (aRNA) was purified using the RNeasy Mini Kit (Qiagen), and the purified aRNA was Cy3 labeled by a reverse transcription reaction as earlier described by Puskas LG, Zvara A, Hackler L, Van Hummelen P: RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 2002, 32(6):1330-1340.


title: 147h vs. 171h Sample_3255


title: 219h vs. 27h Sample_3258


title: 195h vs. 219h Sample_3257


title: 75h vs. 99h Sample_3252


title: 99h vs. 123h Sample_3253


title: 51h vs. 75h Sample_3251


title: 5F7 vs 5F31


title: 219h vs. 27h Sample_3268

description: RNA sampled during four 10-day spontaneous spelt sourdough fermentations with daily back-slopping carried out in the laboratory.


title: 27h vs 51h Sample_3250


title: 195h vs. 219h Sample_3267


title: 219h vs. 27h  Sample_3167


title: 171h vs. 195h Sample_3266


title: 147h vs. 171h Sample_3265


title: 5M21 vs 5F31


title: 5F31 vs 5M21


title: 195h vs. 219h Sample_3166


title: 5F31 vs 5F7


title: 123h vs. 147h Sample_3264


title: 99h vs. 123h Sample_3263


title: 171h vs. 195h Sample_3165


title: 147h vs. 171h Sample_3164


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 22 (Nsp)

type: genomic

city: Lund

first: Henrik

last: Lilljebjörn

address: Lund University Hospital

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Hybridized to 250K_Nsp

hyb_protocol: The protocol provided by the manufacturer (Affymetrix) was used

scan_protocol: The chips were washed and stained according to the manufacturer's instructions and scanned using a GeneChip Scanner 3000

data_processing:
CEL files containing raw signal intensities were exported from the GeneChip Operating Software. The CEL files were imported into GeneChip Genotyping Analysis Software to produce genotype calls using the BRLMM algorithm (CHP-files).
Signal: Summarized signal; Call = Genotype Call (SNP call): AA, AB, BB, and NoCall

molecule: genomic DNA

growth_protocol: The cell line was grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from leukemic blasts obtained from bone marrow at diagnosis using standard methods. Genomic DNA from the REH cell line was extracted from cultured cells using standard methods. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

value: Acute lymphoblastic leukemia


title: 51h vs. 75h Sample_3261


title: 75h vs. 99h Sample_3473


title: 123h vs. 147h Sample_3259


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, REH cell line (Nsp)

description: Hybridized to 250K_Nsp

label_protocol: The protocol provided by the manufacturer (Affymetrix) was used

value: REH


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 20 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 19 (Nsp)

description: Hybridized to 250K_Nsp


title: 99h vs. 123h Sample_2849


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 23 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 21 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 17 (Nsp)

description: Hybridized to 250K_Nsp


title: 27h vs. 99h Sample_3162


title: 219h vs. 27h Sample_2829

tag: fermentation

tag: flour type

value: wheat

tag: depositor


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 18 (Nsp)

description: Hybridized to 250K_Nsp


title: 27h vs. 51h Sample_3260


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 11 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 9 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 16 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 12 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 15 (Nsp)

description: Hybridized to 250K_Nsp


title: 123h vs. 147h Sample_2825


title: 195h vs. 219h Sample_2828


title: 171h vs. 195h Sample_2827


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 13 (Nsp)

description: Hybridized to 250K_Nsp


title: 123h vs 147h Sample_3254


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 10 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 7 (Nsp)

description: Hybridized to 250K_Nsp


title: 99h vs. 123h Sample_2824


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 8 (Nsp)

description: Hybridized to 250K_Nsp


title: 75h vs. 99h Sample_2823


title: 51h vs. 75h Sample_2822


title: 4T1 tumor treated with TKI258, biological replicate 2

city: Basel

first: Julien

middle: Herve

last: Dey

address: Maulbeerstrasse

department: growth control

country: Switzerland

institute: FMI

description: gene expression data from 4T1 tumors after 14 days of treatment with TKI258

hyb_protocol: Biotinylated, fragmented cRNA was hybridized to Affymetrix Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA, USA)

scan_protocol: Standard Affymetrix procedures

data_processing: The data analysis and gene filtering was performed using R/Bioconductor. Signal condensation was performed using only the RMA from the Bioconductor Affy package. Differentially expressed genes were identified using the empirical Bayes method (F-test) implemented in the LIMMA package and adjusted with the False Discovery Rate (FDR) method. Hierarchical clustering and visualization was performed in R. Probe sets with a Log2 average contrast signal of at least 5, an adjusted p-value < 0.05 and an absolute Log2 fold change of > 0.585 (1.5-fold in linear space) were selected.

source_name: tumors from 4T1 cells after 14 days of treatment with TKI258

label_protocol: RNA from TKI258- or water- treated 4T1 tumors was amplified and labeled using the Ambion MesageAMP III RNA Amplification Kit (Applied Biosystems)

growth_protocol: 750000 cells in 75ml PBS were injected in the 4th mammary gland of Balb/C mice.

extract_protocol: At the end of the experiment, tumors were removed and snap frozzen. RNA extraction was performed following extraction with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturers’s protocol. RNAs were washed using the RNeasy Mini Kit (Qiagen) and treated with RNase-free DNase set (Qiagen)

treatment_protocol: 7 days after tumor cell injection, the mice were randomized in the different groups and oral treatment with water or TKI258 (40mg/kg) was performed daily for 14 days.

value: 4T1 tumor

tag: agent


title: 4T1 tumor treated with TKI258, biological replicate 1


title: 4T1 tumor treated with TKI258, biological replicate 3


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 4 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 6 (Nsp)

description: Hybridized to 250K_Nsp


title: 5F31_5F7_27033_1_1


title: 4T1 tumor treated with water, biological replicate 3

description: gene expression data from 4T1 tumors after 14 days of treatment with water

source_name: tumors from 4T1 cells after 14 days of treatment with water

value: water


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 14 (Nsp)

description: Hybridized to 250K_Nsp


title: 27h vs. 51h Sample_2821


title: 4T1 tumor treated with water, biological replicate 1


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 5 (Nsp)

description: Hybridized to 250K_Nsp


title: 4T1 treated with TKI258, biological replicate 3

description: gene expression data from 4T1 cells after 16 hours of TKI258 treatment

source_name: 4T1 cells treated 16h with TKI258

label_protocol: RNA from TKI258- or vehicle- treated 4T1 cells was amplified and labeled using the Ambion MesageAMP III RNA Amplification Kit (Applied Biosystems)

growth_protocol: 750000 cells were seeded in 10cm dish and cultured in DMEM supplemented with 10% FCS for 24 hours.

extract_protocol: RNA was extracted using the Qiashredder and RNeasy Mini Kit coupled with RNase-free DNase set following the manufacturer’s instructions.

treatment_protocol: 24 hours after seeding, the medium was removed from the cells and was changed for DMEM supplemented with 10% FCS and 500nM TKI258 or the vehicle DMSO. The cells were kept 16 hours with these conditions

value: 4T1 cells


title: OD00079_HCP3_N2_MXEMB_4 extraction4_array3

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: OD00079 HCP3;target name: HCP-3;host: Rabbit;antigen: N-terminal histone tail of HCP-3;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Desai Lab;reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55;short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v2. Array scanning and raw data extraction were performed according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software v2.5 according to the NimbleScan User?s Guide.

data_processing:
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180

label: Cy3 dye

organism: Caenorhabditis elegans

growth_protocol: Worm_embryo_growth_and_harvest_vRG1. Synchronized worm cultures were grown at 20 °C in batches of 500 ml using 2.8-L Fernbach flasks shaking at 230 rpm. Gravid adults were separated from debris by sucrose floating. Embryos were isolated by bleaching and fixed after chitinase treatment with 1 % formaldehyde for 10 min on ice. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vRG1. Fixed embryos were suspended in 5 volumes of ChIP buffer (50 mM Hepes-KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) and sonicated on ice with a Branson sonifier microtip (30 % power setting for 3 min; 40 % power setting for 1 min).  Debris were pelleted at 10 000 g for 20 min and the supernatant was made 10 % in glycerol.  The extract was snap frozen in liquid nitrogen aliquots containing 3 mg of protein and stored at ? 80 °C.
Worm_chromatin_immunoprecipitation_vRG1. For each ChIP reaction, 3 mg of protein extract was diluted with ChIP buffer (50 mM Hepes KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) to 900 ?l.  Then 35 ?l 30 % sarcosyl (1 % final) and 20 ?l 5 % Na-deoxycholate (0.1 % final) were added.  50 ?l of the diluted extract were removed (input sample), mixed with Elution buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 250 mM NaCl, 1 % SDS) and processed as described for ChIP samples.  100 ?l antibody/bead suspension (5?g antibody pre-bound to 50 ?l Dynabeads, suspended in ChIP buffer) was added and the mixture and rotated over night at 4 °C.  Beads were washed with 2 × 1 ml FA Buffer (50 mM Hepes-KOH pH 7.6, 150 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 5 min each; with 1 ml FA-1000 buffer (50 mM Hepes-KOH pH 7.6, 1 M NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml FA-500 buffer (50 mM Hepes-KOH pH 7.6, 500 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% NP-40, 1% Na-deoxycholate) for 10 min; and briefly with 1 ml TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA).  Immunocomplexes were eluted with 50 ?l Elution buffer for 15 min at 67 °C.  Eluates were incubated over night at 65 °C to reverse cross-links, then treated with proteinase K (0.44 mg/ml) at 37 °C for 2 h.  Nucleic acids were recovered by phenol/chloroform extraction and ethanol precipitation.  After digestion with RNAse A (0.33 mg/ml) for 2h at 37 °C, DNA was purified using the Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_vRG1. ChIP and input DNA was blunt ended with T4 polymerase for 20 min at 12 °C and purified by phenol/chloroform extraction and EtOH precipitation. Annealed oligonucleotide linkers (oligo 1: gcggtgacccgggagatctgaattc; oligo 2: gaattcagatc) were ligated to the DNA fragments over night at 16 °C. The ligated DNA was precipitated with EtOH, disolved in 10 mM Tris-HCl pH 8, and amplified with a Taq/Pfu polymerase mix using oligo 1. For a detailed protocol see http://www.modencode.org/.

tag: developmental stage

value: Mixed Embryo

tag: genotype

value: wild type

tag: sex

value: mixed Male and Hermaphrodite population

label: Cy5 dye


title: 4T1 treated with TKI258, biological replicate 2


title: OD00079_HCP3_N2_MXEMB_3 extraction3_array3

label_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.


title: 4T1 treated with TKI258, biological replicate 1


title: OD00079_HCP3_N2_MXEMB_2 extraction2_array3

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: OD00079 HCP3;target name: HCP-3;host: Rabbit;antigen: N-terminal histone tail of HCP-3;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Desai Lab;reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55;short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen;
channel ch2 is input DNA;


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 2 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 3 (Nsp)

description: Hybridized to 250K_Nsp


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 1 (Nsp)

description: Hybridized to 250K_Nsp


title: 5F7_5F31_27033_2


title: 4T1 treated with DMSO, biological replicate 2

description: gene expression data from 4T1 cells after 16 hours of DMSO treatment

source_name: 4T1 cells treated 16h with DMSO

value: DMSO


title: 4T1 treated with DMSO, biological replicate 1


title: ABAB5408_4H8_N2_MXEMB_2 extraction2_array3

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab5408;target name: RNA polymerase II CTD repeat YSPTSPS;host: Mouse;antigen: Synthetic peptide YSPTSpPS;clonal: Monoclonal;purified: Protein A/G;company: Abcam;catalog: ab5408;reference: Abcam website and references therein;short description: This antibody recognises the C-terminal repeat of the largest subunit of RNA polymerase II.  It recognises both unphosphorylated and phosphorylated forms.;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.


title: 5M21_5F31_27033_4


title: ABAB5408_4H8_N2_MXEMB_1 extraction1_array3

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab5408;target name: RNA polymerase II CTD repeat YSPTSPS;host: Mouse;antigen: Synthetic peptide YSPTSpPS;clonal: Monoclonal;purified: Protein A/G;company: Abcam;catalog: ab5408;reference: Abcam website and references therein;short description: This antibody recognises the C-terminal repeat of the largest subunit of RNA polymerase II.  It recognises both unphosphorylated and phosphorylated forms.;
channel ch2 is input DNA;

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.


title: 4T1 treated with DMSO, biological replicate 3


title: Primary_Colorectal_Cancer_Patient_No.21

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

description:
HD779-Tu
239731.gpr

hyb_protocol: Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 h at 37°C. Slides were washed with 2x SSC/0.05% Tween-20 at 37°C for one cycle, 2x SSC/0.05% Tween-20 at 44°C for two cycles, 50% formamide/2x SSC/0.1% Tween-20 at 44°C for 3 cycles, 2x SSC/0.05% Tween-20 at 44°C for 2 cycles, and finally 1x PBS/0.05% Tween-20 at 25°C for two cycles. Slides were dried by centrifugation

scan_protocol: Arrays were scanned with an Agilent DNA microarray scanner (Agilent Technologies, Palo Alto, USA), Images were quantified using GenePix Pro 6.0 software (Axon Instruments, Burlingame, USA)

data_processing: Data were filtered consistently according to spot signal/local background ratio (>3.0), mean/median spot intensity (<0.3) and spot replicate standard deviation (<0.25), and normalized globally by print-tip loess

source_name: Primary Colorectal Cancer

label_protocol: 300 ng of genomic DNA was labeled with Cy5 or Cy5 using the Bioprime Labelling Kit (Invitrogen, Karlsruhe, Germany) according to the manufactures' instructions

extract_protocol: Extraction of high molecular weight DNA and RNA from frozen HCC samples was carried out by ultracentrifugation in cesium chloride as previously described in van den Boom et al., 2003 Am J Pathol.

source_name: lymphocyte pool of six healthy male controls


title: Control_Unmethylation DNA_b3

city: Philadelphia

first: IAN

middle: D.

last: KRANTZ

state: PA

address: 34th and Civic Blvd.

department: Division of Human and Molecular Genetics

institute: The Children's Hospital of Philadelphia

description:
4564612047_K

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

hyb_protocol: Standard Illumina protocol for Human Methylation28 DNA Analysis bead chip  Standard Illumina protocol for Human Methylation28 DNA Analysis bead chip  Standard Illumina protocol for Human Methylation28 DNA Analysis bead chip

scan_protocol: Standard Illumina protocol for Human Methylation29 DNA Analysis bead chip  Standard Illumina protocol for Human Methylation29 DNA Analysis bead chip

data_processing: Standard Illumina protocol for Human Methylation29 DNA Analysis bead chipAverage normalization was used to rescale intensities across multiple chips (Methylation, 3.1.0, BeadStudio Methylation Analysis Module). Beta value represents methylation level of the CpG locus using the ratio of intensities between methylated and unmethylated alleles. ß-value was processed by BeadStudio using the implemented procedures. A ß-value of 0-1.0 was reported significant percent methylation, from 0% to 100%, respectively, for each CpG site.  We re-processed the BeadStudio output later on using log2 [β /(1- β )] for further analysis: log2 [β /(1- β )] values given only for the 63 experimental samples.

source_name: Control_Unmethylation DNA_b3

label_protocol: Standard Illumina protocol for Human Methylation27 DNA Analysis bead chip

growth_protocol: Lymphoblastoid cell lines (LCL) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine as described previously.  All 63 cell lines were grown anonymously and processed randomly.

extract_protocol: DNA was extracted from actively growing lymphoblastoid cells using kit from Gentra Systems following the manufacturer’s instruction.

treatment_protocol: Prior to hybridization, bisulfite conversion of DNA samples was done using the EZ DNA methylation kit (Zymo Research).  500ng DNA was used,  a thermocycling program with a short denaturation step included for bisulfite conversion (16 cycles of 95ºC for 30 seconds fol¬lowed by 50ºC for 1 hour)

tag: disease severity

tag: gene mutation

tag: mutation type

tag: id


title: Unaffected (healthy control): GIA-001-S

description:
4564612047_H

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Unaffected (healthy control)

value: F


title: Unaffected (healthy control): CDL-362-06F

description:
4564612047_J

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M


title: Unaffected (healthy control): AGS-365-S

description:
4564612047_I

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M?


title: 147h vs. 171h Sample_2826


title: Liver_Metastasis_Patient_No.21

description:
HD779-LM
238453.gpr

source_name: Liver metastasis of Colorectal Cancer

tag: lymphocyte pool of six healthy male controls


title: Unaffected (healthy control): 95-1681-B

description:
4564612047_L

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: Unaffected (healthy control): 95-3991-S

description:
4564612047_F

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: Genome-wide occupancy of Rpo21p (ORF19.7655)

city: Montreal

first: Adnane

last: Sellam

state: Quebec

address: 6100 Royalmount

department: Anatomy and Cell Biology

institute: Adnane Sellam

description: Starting from sequences from the C. albicans Genome Assembly 21, we extracted a continuous series of 242,860 60-bp oligonucleotides each overlapping by 1 bp. We then eliminated 2062 probes containing stretches of 13 or more A or T nucleotides. The remaining 240,798 sequences were then used to produce sense (Watson) and antisense (Crick) whole genome tiling arrays using the Agilent Technologies eArray service (https://earray.chem.agilent.com/earray/).

hyb_protocol: For gene expression profiling and ChIP-Chip, microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done with an Advalytix SlideBooster. The slides were washed twice with 1X SSC-0.2% SDS and 3 times with 0.1X SSC.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 5-µm resolution for both expression and ChIP-chip experiments.

data_processing:
ChIP-Chip data was normalized as described by Lavoie et al. (2010) PLoS Biol 8(3): e1000329.
Precise peak location and detection from normalized tiling array data was performed by (1) applying a Gaussian blur to log2 fold enrichment ratios, (2) interpolating oligonucleotide probe data to each base pair by a natural spline function, and (3) defining discrete peaks by sequentially extracting the most intense 1 bp peaks and masking a neighboring window of 600 bp (10 probes). Significant peaks were defined as having an enrichment value superior by at least two standard deviations (Z score = 2.0) to the mean of raw probe fold enrichment distributions defined individually for each experiment.

In this study, we performed peak detection only for RNA Polymerase III (Rpc82p). All detected peaks and their genomic features are included as a supplementary file on the Sample record (GSM561024).

organism: Candida albicans

source_name: SN148 under yeast conditions (30°C, YPD)

label_protocol:
cDNA labeling and microarray production were performed as described by Nantel et al. (2006) Medical Mycology: Cellular and Molecular Techniques, Wiley Press.  Briefly, 20 µg of total RNA was reverse transcribed using 9 ng of oligo(dT)21 and 15 ng of random octamers (Invitrogen) in the presence of Cy3 or Cy5-dCTP (Invitrogen) and 400 U of Superscript III reverse transcriptase (Invitrogen). Actinomycin D (ActD) was used to inhibit synthesis of the second cDNA strand to final concentration of 6 µg/ml.

For ChIP-chip samples, test samples were labeled with Cy5 and reference with Cy3.

growth_protocol: For ChIP-chip experiments, RPA190 (ORF19.1839), RPC82 (ORF9.2847), RPB3 (ORF19.1248) and RPO21 (ORF19.7655) were TAP-tagged in vivo with a TAP-URA3 PCR product as describe by Lavoie et al. BMC Genomics 2008, 9:578. Cells were grown to an OD600nm of 2 in 40 ml of YPD.

extract_protocol: ChIP-chip experiment was performed as described by by Lavoie et al. BMC Genomics 2008, 9:578. Chromatin immunoprecipitation was performed by following the protocol available at http://www.ircm.qc.ca/microsites/francoisrobert/en/317.html with the following exceptions: chromatin was sonicated to an average 300 bp, and 700 μl of whole-cell extract (WCE) were incubated with IgG-Sepharose 6 beads Fast Flow (GE Healthcare, catalog number 17-0969-01beads).

tag: genotype/variation

value: TAP-tagged Rpo21p (ORF19.7655)

tag: growth condition

value: yeast conditions (30°C, YPD)

tag: strain

source_name: AS52 under yeast conditions (30°C, YPD)


title: Genome-wide occupancy of Rpb3p (ORF19.1248) (ORF19.1839)

source_name: AS51 under yeast conditions (30°C, YPD)


title: Genome-wide occupancy of Rpc82p (ORF19.2847)

value: TAP-tagged Rpc82p (ORF19.2847)

source_name: AS53 under yeast conditions (30°C, YPD)


title: Liver_Metastasis_Patient_No.20

description:
HD766-LM
239732.gpr


title: Primary_Colorectal_Cancer_Patient_No.20

description:
HD766-Tu
239729.gpr


title: Primary_Colorectal_Cancer_Patient_No.19

description:
HD713-Tu
239237.gpr


title: Unaffected (healthy control): 95-3988-S

description:
4564612047_G

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

tag: gender


title: Liver_Metastasis_Patient_No.19

description:
HD713-LM
239727.gpr


title: mildly affected NIPBL mutant CdLS proband: 190P

description:
4564612047_E

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: Mild

value: NIPBL

value: Missense


title: Genome-wide occupancy of RPA190p (ORF19.1839)

value: TAP-tagged RPA190p (ORF19.1839)

source_name: AS50 under yeast conditions (30°C, YPD)


title: Yeast vs Hyphae_Crick

data_processing:
Fluorescence intensities were quantified using ImaGene software (BioDiscovery Inc.).
A background value was established for every channel of all transcription mapping on the tiling arrays based on the 95th percentile of the distribution of the median expression level of unannotated non-conserved regions of the genomes. In all, 3178 regions spanning at least 3 probes (>180bp) were used to establish this stringent detection threshold. Furthermore, an annotated feature (ORF, RNA or retrotransposons) was considered expressed only if both Cy3 and Cy5 channels mean expression levels were both above their respective threshold level.

source_name: SC5314 under yeast conditions (30°C, YPD)

label_protocol: cDNA labeling and microarray production were performed as described by Nantel et al. (2006) Medical Mycology: Cellular and Molecular Techniques, Wiley Press.  Briefly, 20 µg of total RNA was reverse transcribed using 9 ng of oligo(dT)21 and 15 ng of random octamers (Invitrogen) in the presence of Cy3 or Cy5-dCTP (Invitrogen) and 400 U of Superscript III reverse transcriptase (Invitrogen). Actinomycin D (ActD) was used to inhibit synthesis of the second cDNA strand to final concentration of 6 µg/ml.

growth_protocol: For gene expression profiling of yeast form cells, saturated overnight cultures of the SC5314 strain were diluted to a starting OD600 of 0.1 in 50 ml fresh YPD and grown at 30°C to an OD600 of 0.8. Hyphae were induced by growing Candida cells in YPD+ 10 % fetal bovine serum (FBS) at 37°C to an OD600 of 0.8. Cultures were harvested by centrifugation at 3000 x g for 5 min, and the pellet rapidly frozen in liquid nitrogen.

extract_protocol: RNAs from hyphae, yeast and biofilm were extracted as described by Sellam et al. (2009) Eukaryotic Cell 8 (8), 1174–1183, using RNeasy Mini kit (Qiagen).

source_name: SC5314 under hyphae conditions (10% FBS, 37°C)

value: hyphae conditions (10% FBS, 37°C)


title: mildly affected NIPBL mutant CdLS proband: 181P

description:
4564612047_D

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: Yeast vs Hyphae_Crick_ without Actinomycin D

source_name: WT under hyphae conditions (10% FBS, 37°C, 3 hours)


title: Yeast vs Biofilm_Crick

source_name: SC5314 under Biofilm conditions ( 37°C, YPD)

growth_protocol: Biofilms were grown in RPMI medium at 37°C as described by Nobile et al. (2009) PLoS Biol 2009, 7(6):e1000133.

value: Biofilm conditions ( 37°C, YPD)


title: Yeast vs Caecum grown cells_Crick

source_name: SC5314 grown on mouse caecum

growth_protocol: For RNA extracted from caecum-grown cells, female C57BL/6 mice (5-7 weeks old) were treated with tetracycline (1 mg/ml), streptomycin (2 mg/ml) and gentamicin (0.1 mg/ml) added to their drinking water for the duration of the experiment, beginning 4 days prior to inoculation. C. albicans cells (5x107 cells) were orally inoculated into the mice by gavage. Three days post-inoculation, the mice were sacrificed and the contents of the caecum were recovered and frozen in RNALater (Ambion) at –80°C.

extract_protocol: RNA from caecum was extracted by bead beating with 0.5 mm zirconia/silica beads in TRIzol (Invitrogen). After the TRIzol RNA purification procedure described by the manufacturer, RNA was further purified on Qiagen columns with on-column DNase treatment.

value: grown on mouse caecum


title: severly affected NIPBL mutant CdLS proband: CDL-198-04P

description:
4564612047_C

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: Severe

value: Frameshift


title: Yeast vs Biofilm_Watson

source_name: SC5314 under Biofilm conditions (37°C, YPD)

value: Biofilm conditions (37°C, YPD)


title: SMC1A mutant CdLS proband: CDL-174-04P

description:
4564612047_B

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: SMC1A mutant CdLS proband

value: mild


title: Primary_Colorectal_Cancer_Patient_No.18

description:
HD687-Tu
218663.gpr

source_name: Primary Colorectal Cancer


title: N402 day 8 maltose limited retentostat bioreactor culture / biological replicate # 3

city: Leiden

first: Benjamin

middle: M.

last: Nitsche

state: The Netherlands

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, staining and scanning of the chips. The Affymetrixprotocols are strictly followed. The Affymetrix custom Aspergilus niger Genome Arrays are used for hybridization. To the 270 μl hybridization cocktail, 30 μl labeled material is added according the manual of the Affymetrix One Cycle Target Labeling Kit.

scan_protocol: Standard Affymetrix protocol

data_processing: We used the Mas5 algorithm (as implemented in Genedata Expressionist Pro 4.5) for preprocessing of .CEL files. Genes with detection calls of present (p<0.04) or marginal (0.04<=p<0.06) in at least one of three replicate measurements were accepted as expressed and used in further analyses. Raw signal values were subjected to scaling normalization to the arithmetic mean of a reference group (Day 0 sample) prior to comparison.

organism: Aspergillus niger

source_name: Mycelial biomass day 8 maltose limited bioreactor retentostat culture

label_protocol: The Affymetrix One-Cycle Target Labeling Kit and Control Reagents (#900493) are used to synthesize Biotin-labeled cRNA. From each RNA sample 2 μg is used for the labeling experiments.

growth_protocol: see Treatment Protocol

extract_protocol: Total RNA was isolated from homogenized mycelial samples using TRIzol reagent (Invitrogen).

treatment_protocol:
Strain and inoculum:
Aspergillus niger N402 (cspA), a standard laboratory strain with short conidiophores (Bos et al., 1988), was propagated on solidified Complete Medium (CM) to produce conidial inoculum for submerged cultivation. CM agar plates contained (per liter):10.0 g glucose, 6.0 g NaNO3, 1.5 g KH2PO4, 0.5 g KCl, 0.5 g Mg SO4∙7H2O, 1.0 g casamino acids, 5.0 g yeast extract, 20 g agar and 1 ml trace metal solution. The trace metal solution contains per liter, 10 g EDTA, 4.4 g ZnSO4⋅7H2O, 1.01 g MnCl2⋅4H2O, 0.32 g CoCl2⋅6H2O, 0.315 g CuSO4⋅5H2O, 0.22 g (NH4)6Mo7O24⋅4H2O, 1.47 g CaCl2⋅2H2O and 1 g FeSO4⋅7H2O (modified from composition given by Vishniac and Santer, 1957). pH of the medium was adjusted to 5.8 with NaOH prior to autoclaving. The solid medium cultures were incubated for at least 6 days at 30 °C to allow adequate conidium formation. Spore plates were stored for no more than three months at 4 °C. For preparation of inoculum, conidia were harvested and washed with a sterile detergent solution containing 0.05 % (w/v) Tween 80 and 0.9 % (w/v) NaCl.
Batch cultures:
Bioreactors holding 5 liter (kg) Minimal Medium (MM) was inoculated with conidial suspension to give 109 conidia L-1. The MM contained (per liter): 4.5 g NH4Cl, 1.5 g KH2PO4, 0.5 KCl, 0.5 MgSO4⋅7H2O and 1 ml trace metal solution (described above). pH was adjusted to 3. The final-cell-density-limiting (growth-limiting) substrate was 4 g maltose (monohydrate) per liter. Concentrated solutions (20x) of carbon source were heat sterilized separately and added aseptically to sterile MM. During cultivation, temperature was 30 °C and pH 3, kept constant by computer controlled addition of 2 M NaOH or 1 M HCl. Sterile air was supplied at 1 L min-1 through a ring-sparger. Dissolved oxygen tension was above 40% of air saturation at anytime, ensuring oxygen sufficient growth. Germination of the dormant conidia was induced by addition 0.003% (w/w) yeast extract before inoculation. During the first six hours of cultivation, the culture was aerated through the headspace of the reactor and stirrer speed was kept low at 250 rpm. These precautions minimized gas-liquid interface, thereby reducing loss of hydrophobic conidia to the exhaust gas. After six hours and germination of most conidia (now hydrophilic), air was sparged into the culture broth and mixing intensified (750 rpm) for more efficient mass transfer. At this stage, 0.01% (v/v) PPG was added as antifoam agent. Submerged cultivation was performed with 6.6 L BioFlo3000 bioreactors (New Brunswick Scientific, NJ, USA). Culture mass was monitored with a Mettler Toledo KCC150s scale, which has a maximum load capacity of 150 kg and an accuracy of 10g. The glass surface of the head space was cooled to minimize wall growth.
Cell retention:
A special cell retention device (FIG. 1A) was developed to enable efficient separation of filamentous biomass and allow reliable operation of retentostat cultures (this study). The retention principle is simple (FIG. 1B,C). Dilute culture broth rises, by unforced filtration over a coarse filter, into a cylinder inserted from the top-plate (through existing 19mm injection port). The dilute is constantly drained from the cylinder, thereby maintaining constant culture volume. The vertical position of the filter can be adjusted aseptically to facilitate filtration as biomass density increases. An anti-fouling mechanism prevents blockage of the filter by intermittent sparging (2s every 12s) sterile air (2 L min-1) through the cylinder and filter. Biomass retention was nearly complete (95-99%) and filtrate could be drained at a rate of at least 0.25 L h-1 (0.19L h-1 per cm2 filter area) at biomass densities of at least 10 g dry weight per liter culture broth. The device was constructed from durable materials with high temperature resistance, this allowed repeated use and heat sterilization. The filter housing (frame and cylinder, 19x200mm) was made of stainless steel, the septum of silicone and drain tubing of Teflon. The filter itself was cut from sheets of Spectra Mesh (Spectrum Laboratories, CA, USA). Stainless steel mesh with pore size of 51 µm and 42% open area was used. The cell retention device was crafted at the BMB work shop (University of Southern Denmark) according to instructions from T. R. J.
Biomass sampling:
Biomass for total RNA extraction was sampled at day 2 after start of retentostat flow.

value: N402 laboratory wild-type


title: Liver_Metastasis_Patient_No.18

description:
HD687-LM
218721.gpr

source_name: lymphocyte pool of six healthy male controls


title: N402 day 8 maltose limited retentostat bioreactor culture / biological replicate # 2


title: Yeast vs Hyphae_Watson

source_name: SC5314 under hyphae conditions (YPD+10% FBS, 37°C)

value: hyphae conditions (YPD+10% FBS, 37°C)


title: severly affected NIPBL mutant CdLS proband: CDL-108-00P

description:
4564612047_A

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: F


title: Liver_Metastasis_Patient_No.17

description:
HD668-LM
218719.gpr

source_name: Liver metastasis of Colorectal Cancer


title: N402 day 2 maltose limited retentostat bioreactor culture / biological replicate # 3

source_name: Mycelial biomass day 2 maltose limited bioreactor retentostat culture


title: Yeast vs Caecum grown cells_Watson


title: Primary_Colorectal_Cancer_Patient_No.17

description:
HD668-Tu
218720.gpr


title: N402 day 8 maltose limited retentostat bioreactor culture / biological replicate # 1


title: Control_Unmethylation DNA_a2

description:
4564612042_K

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Control_Unmethylation DNA_a2


title: Liver_Metastasis_Patient_No.16

description:
HD662-LM
218726.gpr


title: Yeast vs Hyphae_Watson_ without Actinomycin D

value: hyphae conditions (10% FBS, 37°C, 3 hours)


title: SMC1A mutant CdLS proband: CDL-363-06P

description:
4564612042_J

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: 4T1 tumor treated with water, biological replicate 2

description: gene expression data from 4T1 tumors after 14 days of treatment with water

source_name: tumors from 4T1 cells after 14 days of treatment with water

tag: cell type

value: 4T1 tumor

value: water


title: Primary_Colorectal_Cancer_Patient_No.16

description:
HD662-Tu
218724.gpr


title: Primary_Colorectal_Cancer_Patient_No.15

description:
HD590-Tu
218661.gpr

source_name: lymphocyte pool of six healthy female controls


title: N402 day 2 maltose limited retentostat bioreactor culture / biological replicate # 2


title: N402 day 2 maltose limited retentostat bioreactor culture / biological replicate # 1

source_name: Mycelial biomass, early time point, maltose limited bioreactor retentostat culture

treatment_protocol:
Strain and inoculum:
Aspergillus niger N402 (cspA), a standard laboratory strain with short conidiophores (Bos et al., 1988), was propagated on solidified Complete Medium (CM) to produce conidial inoculum for submerged cultivation. CM agar plates contained (per liter):10.0 g glucose, 6.0 g NaNO3, 1.5 g KH2PO4, 0.5 g KCl, 0.5 g Mg SO4∙7H2O, 1.0 g casamino acids, 5.0 g yeast extract, 20 g agar and 1 ml trace metal solution. The trace metal solution contains per liter, 10 g EDTA, 4.4 g ZnSO4⋅7H2O, 1.01 g MnCl2⋅4H2O, 0.32 g CoCl2⋅6H2O, 0.315 g CuSO4⋅5H2O, 0.22 g (NH4)6Mo7O24⋅4H2O, 1.47 g CaCl2⋅2H2O and 1 g FeSO4⋅7H2O (modified from composition given by Vishniac and Santer, 1957). pH of the medium was adjusted to 5.8 with NaOH prior to autoclaving. The solid medium cultures were incubated for at least 6 days at 30 °C to allow adequate conidium formation. Spore plates were stored for no more than three months at 4 °C. For preparation of inoculum, conidia were harvested and washed with a sterile detergent solution containing 0.05 % (w/v) Tween 80 and 0.9 % (w/v) NaCl.
Batch cultures:
Bioreactors holding 5 liter (kg) Minimal Medium (MM) was inoculated with conidial suspension to give 109 conidia L-1. The MM contained (per liter): 4.5 g NH4Cl, 1.5 g KH2PO4, 0.5 KCl, 0.5 MgSO4⋅7H2O and 1 ml trace metal solution (described above). pH was adjusted to 3. The final-cell-density-limiting (growth-limiting) substrate was 4 g maltose (monohydrate) per liter. Concentrated solutions (20x) of carbon source were heat sterilized separately and added aseptically to sterile MM. During cultivation, temperature was 30 °C and pH 3, kept constant by computer controlled addition of 2 M NaOH or 1 M HCl. Sterile air was supplied at 1 L min-1 through a ring-sparger. Dissolved oxygen tension was above 40% of air saturation at anytime, ensuring oxygen sufficient growth. Germination of the dormant conidia was induced by addition 0.003% (w/w) yeast extract before inoculation. During the first six hours of cultivation, the culture was aerated through the headspace of the reactor and stirrer speed was kept low at 250 rpm. These precautions minimized gas-liquid interface, thereby reducing loss of hydrophobic conidia to the exhaust gas. After six hours and germination of most conidia (now hydrophilic), air was sparged into the culture broth and mixing intensified (750 rpm) for more efficient mass transfer. At this stage, 0.01% (v/v) PPG was added as antifoam agent. Submerged cultivation was performed with 6.6 L BioFlo3000 bioreactors (New Brunswick Scientific, NJ, USA). Culture mass was monitored with a Mettler Toledo KCC150s scale, which has a maximum load capacity of 150 kg and an accuracy of 10g. The glass surface of the head space was cooled to minimize wall growth.
Cell retention:
A special cell retention device (FIG. 1A) was developed to enable efficient separation of filamentous biomass and allow reliable operation of retentostat cultures (this study). The retention principle is simple (FIG. 1B,C). Dilute culture broth rises, by unforced filtration over a coarse filter, into a cylinder inserted from the top-plate (through existing 19mm injection port). The dilute is constantly drained from the cylinder, thereby maintaining constant culture volume. The vertical position of the filter can be adjusted aseptically to facilitate filtration as biomass density increases. An anti-fouling mechanism prevents blockage of the filter by intermittent sparging (2s every 12s) sterile air (2 L min-1) through the cylinder and filter. Biomass retention was nearly complete (95-99%) and filtrate could be drained at a rate of at least 0.25 L h-1 (0.19L h-1 per cm2 filter area) at biomass densities of at least 10 g dry weight per liter culture broth. The device was constructed from durable materials with high temperature resistance, this allowed repeated use and heat sterilization. The filter housing (frame and cylinder, 19x200mm) was made of stainless steel, the septum of silicone and drain tubing of Teflon. The filter itself was cut from sheets of Spectra Mesh (Spectrum Laboratories, CA, USA). Stainless steel mesh with pore size of 51 µm and 42% open area was used. The cell retention device was crafted at the BMB work shop (University of Southern Denmark) according to instructions from T. R. J.
Biomass sampling:
Biomass for total RNA extraction was sampled 2 days after start of retentostat cultivation.


title: Liver_Metastasis_Patient_No.15

description:
HD590-LM
218662.gpr

tag: lymphocyte pool of six healthy female controls


title: severly affected NIPBL mutant CdLS proband: CDL-173-04P

description:
4564612042_I

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M


title: STyphimurium_IR715(pWSK29)_vs_IR715(pTVIA1)_lowsalt

city: Davis

first: Sebastian

last: Winter

state: CA

address: One Shields Ave

department: MMI

institute: UC Davis

description: Comparison between a tviA expressing S. Typhimurium strain and the wild-type strain to assess effect of regulatory gene tviA on global gene expression.

hyb_protocol: Seo YS, Sriariyanun M, Wang L, Pfeiff J, Phetsom J, Lin Y, Jung KH, Chou HH, Bogdanove A, Ronald P. A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes. BMC Microbiol. 2008 Jun 18;8:99. PMID 18564427

data_processing:
For raw data processing and analysis, the TM4 Microarray Software Suite was used. Local background intensity was substracted from each itensity value. Raw expression data were normalized using a global Locfit/LOWESS algorithm. The dye flip (two technical replicates) was corrected (TM4 Microarray Software Suite).  Replicates on each array were combined by averaging the fold change of each gene.
Photomultiplier setting (HI: high intensity, LI low intensity): Data from both scans was processed (local background subtraction, normalization, in-slide replicates averaged). Then HI and LI were compared. If the intensity value of any channel (Ch1 or Ch2) in the high intensity scan was higher than 32000 (half of the maximum value), all information was replaced with that from the low intensity scan (values <32000).

label: Alexa Fluor 555

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium IR715(pWSK29) low salt

label_protocol: cDNA was synthesized and differentially labeled using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen)

growth_protocol: The S. Typhimurium strain was grown in SOB broth to mid-log phase (OD600 = 0.4-0.5) statically at 37C

extract_protocol: S. Typhimurium strains were grown in 5 ml broth. 0.8 ml stop solution (5 % water saturated phenol in ethanol) was added and the suspension centrifuged at 7,700 g for 5 min at 4°C. The bacterial pellet was resuspended in 0.4 ml lysis solution (0.1 mg/ml lysozyme, 1mM EDTA 10mM, Tris/Cl pH = 8.0) and the suspension incubated at 25°C for 1 h. Next, 40 μl 10 % SDS was added and the solution heated to 65°C. After 2 min, 0.44 ml 1 M sodium acetate and 0.9 ml hot (65°C) phenol was added to the sample. The emulsion was incubated at 65°C for 6 min, chilled on ice for 10 min and centrifuged at 20,000 g for 10 min at 4°C. The aqueous phase was transferred to a new tube, extracted with 0.9 ml chloroform. Phases were separated by centrifugation at 20,000 g for 5 min at 4°C. After transferring the upper aqueous phase to a new tube, the RNA was precipitated by adding 80 μl 1 mM EDTA 3 M sodium acetate pH = 5.2 and 1 ml isopropanol. The samples were centrifuged for 30 min at 20,000 g at 4°C and the supernatant discarded. The RNA pellet was washed with 1 ml 80 % Ethanol and the samples were centrifuged for 5 min at 20,000 g at 4°C. RNA was air-dried and resuspended in RNase-free water. Traces of DNA in the RNA preparation were removed by DNase treatment (DNA-free DNase treatment, Applied Biosystems).

value: S. Typhimurium IR715 harboring cloning plasmid pWSK29 ( PMID:2055470; PMID:7868611)

label: Alexa Fluor 647

source_name: S. Typhimurium IR715(pTVIA1) low salt

value: S. Typhimurium IR715 harboring cloning plasmid pTVIA1. pTVIA1 was constructed by cloning the tviA promoter region and the coding sequence from S. Typhi Ty2 into the cloning vector pWSK29.  (PMID:2055470; PMID:7868611; PMID:17591794)


title: Unaffected (healthy control): 95-3985-S

description:
4564612042_L

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Unaffected (healthy control)


title: Control_Methylation DNA_1

description:
4564612042_H

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Control_Methylation DNA_1


title: N402 exponential growth phase maltose limited batch bioreactor culture / biological replicate # 2

source_name: Mycelial biomass, exponential growth phase, maltose limited bioreactor batch culture

treatment_protocol:
Strain and inoculum:
Aspergillus niger N402 (cspA), a standard laboratory strain with short conidiophores (Bos et al., 1988), was propagated on solidified Complete Medium (CM) to produce conidial inoculum for submerged cultivation. CM agar plates contained (per liter):10.0 g glucose, 6.0 g NaNO3, 1.5 g KH2PO4, 0.5 g KCl, 0.5 g Mg SO4∙7H2O, 1.0 g casamino acids, 5.0 g yeast extract, 20 g agar and 1 ml trace metal solution. The trace metal solution contains per liter, 10 g EDTA, 4.4 g ZnSO4⋅7H2O, 1.01 g MnCl2⋅4H2O, 0.32 g CoCl2⋅6H2O, 0.315 g CuSO4⋅5H2O, 0.22 g (NH4)6Mo7O24⋅4H2O, 1.47 g CaCl2⋅2H2O and 1 g FeSO4⋅7H2O (modified from composition given by Vishniac and Santer, 1957). pH of the medium was adjusted to 5.8 with NaOH prior to autoclaving. The solid medium cultures were incubated for at least 6 days at 30 °C to allow adequate conidium formation. Spore plates were stored for no more than three months at 4 °C. For preparation of inoculum, conidia were harvested and washed with a sterile detergent solution containing 0.05 % (w/v) Tween 80 and 0.9 % (w/v) NaCl.
Batch cultures:
Bioreactors holding 5 liter (kg) Minimal Medium (MM) was inoculated with conidial suspension to give 109 conidia L-1. The MM contained (per liter): 4.5 g NH4Cl, 1.5 g KH2PO4, 0.5 KCl, 0.5 MgSO4⋅7H2O and 1 ml trace metal solution (described above). pH was adjusted to 3. The final-cell-density-limiting (growth-limiting) substrate was 4 g maltose (monohydrate) per liter. Concentrated solutions (20x) of carbon source were heat sterilized separately and added aseptically to sterile MM. During cultivation, temperature was 30 °C and pH 3, kept constant by computer controlled addition of 2 M NaOH or 1 M HCl. Sterile air was supplied at 1 L min-1 through a ring-sparger. Dissolved oxygen tension was above 40% of air saturation at anytime, ensuring oxygen sufficient growth. Germination of the dormant conidia was induced by addition 0.003% (w/w) yeast extract before inoculation. During the first six hours of cultivation, the culture was aerated through the headspace of the reactor and stirrer speed was kept low at 250 rpm. These precautions minimized gas-liquid interface, thereby reducing loss of hydrophobic conidia to the exhaust gas. After six hours and germination of most conidia (now hydrophilic), air was sparged into the culture broth and mixing intensified (750 rpm) for more efficient mass transfer. At this stage, 0.01% (v/v) PPG was added as antifoam agent. Submerged cultivation was performed with 6.6 L BioFlo3000 bioreactors (New Brunswick Scientific, NJ, USA). Culture mass was monitored with a Mettler Toledo KCC150s scale, which has a maximum load capacity of 150 kg and an accuracy of 10g. The glass surface of the head space was cooled to minimize wall growth.
Biomass sampling:
Biomass for total RNA extraction was sampled after approximately 75% of the soule limiting carbon source (Maltose 0.8%) was consumed. Consumption of the carbon source was followed by the titrant addition based on a linear correlation.


title: Primary_Colorectal_Cancer_Patient_No.14

description:
HD571-Tu
218659.gpr


title: Unaffected (healthy control): AGS-139-S

description:
4564612042_G

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: N402 exponential growth phase maltose limited batch bioreactor culture / biological replicate # 3


title: Wild Type duodenum, day 30, biological replicate 3

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

description: Mice during postnatal developmental phase of intestine, day 30

hyb_protocol: Following fragmentation, 2.5 ug of cRNA were hybridized for 18 hr at 45C on Affymetrix Mouse Gene 1.0 ST Array in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (protocol FS450-0007). Stained with R-Phycoerythrin Stepavidin (Molecular Probes) and probed with anti-streptavidin biotinylated goat antibody (Vector Laboratories).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G and GeneChip Operating Software.

data_processing: The CEL files were processed through the Affymetrix Expression Console software (ver. 1.1).  These were RMA normalized and the intensity values were used in Genespring GX 7.3.1 to create the experiments.

source_name: Mouse duodenum, Wild type, day 30

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA .

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

treatment_protocol: No treatment

tag: tissue

value: Duodenum

value: Wild type

tag: age

value: Postnatal day 30

value: Mixed


title: BCBL-1 +VA, 48hr replicate 2 (P-type strain study)

city: San Francisco

first: Sanjay

last: Chandriani

address: 513 Parnassus Avenue

institute: UCSF

hyb_protocol: Samples were hybridized to the custom tiling microarrays according the manufacturer’s protocol (Agilent). Hybridized microarrays were washed according to the manufacturer’s protocol (Agilent),

scan_protocol: Microarrays were scanned on the GenePix 4000B scanner (Axon instruments) and all feature intensities collected using the GenePix Pro 6.0 software.

data_processing:
TIFF images of scanned slides were analyzed using Feature Extraction Software version 9.5.3 (Agilent) using a custom grid file (017577_D_F_20070822). LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
Data of identical probes were averaged.
Data were subject to a further linear normalization step by the average of the features detecting the spike-in transcripts. Only features that did not have any feature non-uniformity or population outlier flags contributed to the averages used for determining the normalization factor.
Remove any data that failed any of the following spot quality filters: 1. gIsFound = 1 AND rIsFound = 1; 2. no PopnOL or NonUnifOL detected; 3. g OR r IsWellAboveBackground.
Data of every probe was centered to the average of the corresponding control samples.
Data for host genes were removed and probes against viral sequences were ordered by position in genome.

source_name: BCBL-1 +VA, 48hr replicate 2

label_protocol: The Quick Amp labeling kit (Agilent) was used according to the manufacturer’s protocol to generate Cy5/Cy3 labeled cRNA from 450ng of total RNA, which contains mix of spike-in transcripts A + B (Agilent). An equal amount of hte spike-in transcript mix are added to both Cy5 and Cy3 labeled samples. The spike-in transcripts are detected by E1A probes on the array and are used for a linear normalization subsequent to the LOWESS normalization performed by the Agilent feature extraction software.

extract_protocol: All samples were harvested in RLT buffer and RNA was isolated using the RNeasy Mini kit according to the manufacturer’s protocol (Qiagen)

tag: virus

value: KSHV (P-type strain)

tag: infection status

value: Stable, lytic

source_name: Common reference: mix of several different cell types (BJAB, BCBL, SLK, HFF, HUVEC, TIME), both infected and uninfected.

value: All infections were performed with either BCBL-1-derived KSHV or rKSHV.219.

value: both infected and uninfected


title: Unaffected (healthy control): CDL-043-99S1

description:
4564612042_E

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: BCBL-1 +VA, 48hr replicate 1 (P-type strain study)

source_name: BCBL-1 +VA, 48hr replicate 1

value: mix of several different cell types (BJAB, BCBL, SLK, HFF, HUVEC, TIME)


title: Primary_Colorectal_Cancer_Patient_No.12

description:
HD555-Tu
D31_167760_secondupload.gpr

source_name: Primary Colorectal Cancer


title: BCBL-1 uninduced replicate 2 (P-type strain study)

source_name: BCBL-1 uninduced replicate 2

value: Stable, latent


title: Unaffected (healthy control): CDL-416-07F

description:
4564612042_D

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: 5F31_5M21_27033_3

label_protocol: According to manufacturer's instructions.

extract_protocol: Total RNA extracted using the nucleospin RNA II kit from Macherey-Nagel.


title: Unaffected (healthy control): CDL-312-06F

description:
4564612042_C

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: Liver_Metastasis_Patient_No.12

description:
HD555-LM
D32_168181_secondupload.gpr

source_name: Liver metastasis of Colorectal Cancer


title: Liver_Metastasis_Patient_No.13

description:
HD569-LM
218657.gpr


title: Primary_Colorectal_Cancer_Patient_No.13

description:
HD569-Tu
218845.gpr


title: Wild Type duodenum, day 30, biological replicate 1

tag: genotype


title: Oneut-2 knockout duodenum, day 30, biological replicate 3

source_name: Mouse duodenum, Onecut-2 knockout, day 30

value: Onecut-2 knockout


title: Wild Type duodenum, day 30, biological replicate 2


title: BJAB replicate 2 (P-type strain study)

source_name: BJAB replicate 2

value: BJAB

value: Uninfected


title: Liver_Metastasis_Patient_No.14

description:
HD571-LM
218660.gpr

source_name: lymphocyte pool of six healthy male controls


title: Liver_Metastasis_Patient_No.11

description:
HD536-LM
US22502683_162361_S01_A01.gpr

source_name: lymphocyte pool of six healthy female controls


title: Unaffected (healthy control): CDL-047-99S

description:
4564612042_B

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: F


title: Unaffected (healthy control): 95-3999-B

description:
4564612042_F

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M


title: N402 exponential growth phase maltose limited batch bioreactor culture / biological replicate # 1

treatment_protocol:
Strain and inoculum:
Aspergillus niger N402 (cspA), a standard laboratory strain with short conidiophores (Bos et al., 1988), was propagated on solidified Complete Medium (CM) to produce conidial inoculum for submerged cultivation. CM agar plates contained (per liter):10.0 g glucose,  6.0 g NaNO3, 1.5 g KH2PO4, 0.5 g KCl, 0.5 g Mg SO4∙7H2O, 1.0 g casamino acids, 5.0 g yeast extract, 20 g agar and 1 ml trace metal solution. The trace metal solution contains per liter, 10 g EDTA, 4.4 g ZnSO4⋅7H2O, 1.01 g MnCl2⋅4H2O, 0.32 g CoCl2⋅6H2O, 0.315 g CuSO4⋅5H2O, 0.22 g (NH4)6Mo7O24⋅4H2O, 1.47 g CaCl2⋅2H2O and 1 g FeSO4⋅7H2O (modified from composition given by Vishniac and Santer, 1957). pH of the medium was adjusted to 5.8 with NaOH prior to autoclaving. The solid medium cultures were incubated for at least 6 days at 30 °C to allow adequate conidium formation. Spore plates were stored for no more than three months at 4 °C. For preparation of inoculum, conidia were harvested and washed with a sterile detergent solution containing 0.05 % (w/v) Tween 80 and 0.9 % (w/v) NaCl.
Batch cultures:
Bioreactors holding 5 liter (kg) Minimal Medium (MM) was inoculated with conidial suspension to give 109 conidia L-1. The MM contained (per liter): 4.5 g NH4Cl, 1.5 g KH2PO4, 0.5 KCl, 0.5 MgSO4⋅7H2O and 1 ml trace metal solution (described above). pH was adjusted to 3. The final-cell-density-limiting (growth-limiting) substrate was 4 g maltose (monohydrate) per liter. Concentrated solutions (20x) of carbon source were heat sterilized separately and added aseptically to sterile MM. During cultivation, temperature was 30 °C and pH 3, kept constant by computer controlled addition of 2 M NaOH or 1 M HCl. Sterile air was supplied at 1 L min-1 through a ring-sparger. Dissolved oxygen tension was above 40% of air saturation at anytime, ensuring oxygen sufficient growth. Germination of the dormant conidia was induced by addition 0.003% (w/w) yeast extract before inoculation. During the first six hours of cultivation, the culture was aerated  through the headspace of the reactor and stirrer speed was kept low at 250 rpm. These precautions minimized gas-liquid interface, thereby reducing loss of hydrophobic conidia to the exhaust gas. After six hours and germination of most conidia (now hydrophilic), air was sparged into the culture broth and mixing intensified (750 rpm) for more efficient mass transfer. At this stage, 0.01% (v/v) PPG was added as antifoam agent. Submerged cultivation was performed with 6.6 L BioFlo3000 bioreactors (New Brunswick Scientific, NJ, USA). Culture mass was monitored  with a Mettler Toledo KCC150s scale, which has a maximum load capacity of 150 kg and an accuracy of 10g. The glass surface of the head space was cooled to minimize wall growth.
Biomass sampling:
Biomass for total RNA extraction was sampled after approximately 75% of the soule limiting carbon source (Maltose 0.8%) was consumed. Consumption of the carbon source was followed by the titrant addition based on a linear correlation.

value: N402 laboratory wild-type


title: BCBL-1 uninduced replicate 1 (P-type strain study)

source_name: BCBL-1 uninduced replicate 1


title: Primary_Colorectal_Cancer_Patient_No.11

description:
HD536-Tu
US22502683_161516_S01_A01.gpr


title: Unaffected (healthy control): 95-3986-S

description:
4564612042_A

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: Oneut-2 knockout duodenum, day 30, biological replicate 2


title: BJAB replicate 1 (P-type strain study)

source_name: BJAB replicate 1


title: TIME +KSHV/AdRTA, 54 h.p.i. replicate 2 (P-type strain study)

source_name: TIME +KSHV/AdRTA, 54 h.p.i. replicate 2

value: TIME

value: Acute, lytic


title: Wild Type duodenum, day 15, biological replicate 3

description: Mice during postnatal developmental phase of intestine, day 15

source_name: Mouse duodenum, Wild type, day 15

value: Duodenum

value: Wild type

value: Postnatal day 15


title: Oneut-2 knockout duodenum, day 30, biological replicate 1

value: Postnatal day 30

value: Mixed


title: TIME +KSHV/AdRTA, 54 h.p.i. replicate 1 (P-type strain study)

source_name: TIME +KSHV/AdRTA, 54 h.p.i. replicate 1

value: KSHV (P-type strain)

value: All infections were performed with either BCBL-1-derived KSHV or rKSHV.219.


title: Wild Type duodenum, day 15, biological replicate 2


title: Unaffected (healthy control): CDL-362-06M

description:
4564612037_J

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Unaffected (healthy control)


title: TIME +KSHV, 50 h.p.i. (P-type strain study)

source_name: TIME +KSHV, 50 h.p.i.

value: Acute, latent

value: mix of several different cell types (BJAB, BCBL, SLK, HFF, HUVEC, TIME)

value: both infected and uninfected


title: Primary_Colorectal_Cancer_Patient_No.9

description:
HD524-Tu
US22502683_156878_S01_A01.gpr


title: Liver_Metastasis_Patient_No.10

description:
HD529-LM
US22502683_156882_S01_A01.gpr


title: mildly affected NIPBL mutant CdLS proband: 95-1684-P

description:
4564612037_K

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: Mild

value: NIPBL

value: Missense


title: Primary_Colorectal_Cancer_Patient_No.10

description:
HD529-Tu
US22502683_203961_S01_A01.gpr


title: TIME +KSHV, 36 h.p.i. (P-type strain study)

source_name: TIME +KSHV, 36 h.p.i.


title: Wild Type duodenum, day 15, biological replicate 1


title: Liver_Metastasis_Patient_No.8

description:
HD522-LM
US22502683_156880_S01_A01.gpr


title: Liver_Metastasis_Patient_No.9

description:
HD524-LM
US22502683_156722_S01_A01.gpr


title: TIME +KSHV, 24 h.p.i. (P-type strain study)

source_name: TIME +KSHV, 24 h.p.i.

source_name: Common reference: mix of several different cell types (BJAB, BCBL, SLK, HFF, HUVEC, TIME), both infected and uninfected.


title: Oneut-2 knockout duodenum, day 15, biological replicate 3

source_name: Mouse duodenum, Onecut-2 knockout, day 15

value: Onecut-2 knockout


title: Unaffected (healthy control): 27572-B

description:
4564612037_I

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M