title: 254706910016_b3 - WT.NT.TR1 vs BIG2.NT.TR1

hyb_protocol: BIG2.NT.TR1 Cy5 / WT.NT.TR1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: BIG2.NT.TR1:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: WT.NT.TR1:100mg. (Qiagen_RNeasy.pdf)


title: Patient 3_Normal

status: Public on Sep 01 2016

type: RNA

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

country: USA

institute: 10x Genomics

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Non-fluorescence brain

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by submitter

tag: tissue

value: Non-fluorescence brain


title: 254706910035_b2 - BIG1.NT.TR2 vs WT.NT.TR2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: What are the gene networks associated with BIGUN function during Hyaloperonospora arabidopsidis infection?

hyb_protocol: WT.NT.TR2 Cy5 / BIG1.NT.TR2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - Media: soil Hygrometry: 60% Temperature: 21°C Light: 25 klux

extract_protocol: WT.NT.TR2:100mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: cultivar

value: columbia

value: leaf

tag: genotype

value: wildtype

tag: age

tag: developmental stage (boyes et al. plant cell 2001)

value: boyes 3.90

extract_protocol: BIG1.NT.TR2:100mg. (Qiagen_RNeasy.pdf)

value: bigun 1 mutant


title: Patient 3_Tumoral

source_name: Red fluorescence glioma

value: Red fluorescence glioma


title: 254706910036_b2 - BIG1.NT.TR3 vs WT.NT.TR3

hyb_protocol: WT.NT.TR3 Cy5 / BIG1.NT.TR3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: WT.NT.TR3:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: BIG1.NT.TR3:100mg. (Qiagen_RNeasy.pdf)


title: 254706910036_b1 - WT.NT.TR3 vs BIG1.NT.TR3

hyb_protocol: BIG1.NT.TR3 Cy5 / WT.NT.TR3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910035_b1 - WT.NT.TR2 vs BIG1.NT.TR2

hyb_protocol: BIG1.NT.TR2 Cy5 / WT.NT.TR2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910036_b3 - WT.NT.TR3 vs BIG2.NT.TR3

hyb_protocol: BIG2.NT.TR3 Cy5 / WT.NT.TR3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: BIG2.NT.TR3:100mg. (Qiagen_RNeasy.pdf)

value: bigun 2 mutant


title: 254706910016_b1 - WT.NT.TR1 vs BIG1.NT.TR1

hyb_protocol: BIG1.NT.TR1 Cy5 / WT.NT.TR1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: BIG1.NT.TR1:100mg. (Qiagen_RNeasy.pdf)


title: 254706910036_b4 - BIG2.NT.TR3 vs WT.NT.TR3

hyb_protocol: WT.NT.TR3 Cy5 / BIG2.NT.TR3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910016_b4 - BIG2.NT.TR1 vs WT.NT.TR1

hyb_protocol: WT.NT.TR1 Cy5 / BIG2.NT.TR1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910035_b4 - BIG2.NT.TR2 vs WT.NT.TR2

hyb_protocol: WT.NT.TR2 Cy5 / BIG2.NT.TR2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: BIG2.NT.TR2:100mg. (Qiagen_RNeasy.pdf)


title: 254706910016_b2 - BIG1.NT.TR1 vs WT.NT.TR1

hyb_protocol: WT.NT.TR1 Cy5 / BIG1.NT.TR1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Day 3 Clone 2 eAPC

city: Bethesda

first: Abhishek

middle: K

last: Srivastava

state: MD

address: 10 Center Drive. Room 3-5888

institute: NIH

description: Antigen-specific T cell clones expanded with eAPC

data_processing: Array was performed with Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array (54,575 transcripts). MAS 5

label: biotin

source_name: Antigen specific CD8+ T cell clone from melanoma patients

label_protocol: According to standard Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array protocol

growth_protocol: T cell clones were undergone in vitro expansion in media containing IL-2 (50cu/ml), anti-CD3 antibody (25ng/ml) and irradiated PBMC feeders

extract_protocol: Rneasy kit (Qiagen) used to extract RNA

treatment_protocol: In vitro cultutre were added with either eAPC or eAPC:4-1BBL

tag: cell type

value: CD8+ T cel


title: Day 7 Clone 7 eAPC:4-1BBL

description: Antigen-specific T cell clones expanded with eAPC:4-1BBL


title: Day 7 Clone 8 eAPC


title: Day 3 Clone 4 eAPC:4-1BBL


title: Day 3 Clone 3 eAPC


title: Day 7 Clone 6 eAPC:4-1BBL


title: Patient 1_Normal


title: 685

city: Jacksonville

first: Daniel

last: Serie

state: Florida

address: 4500 San Pablo Rd

institute: Mayo Clinic

hyb_protocol: The products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA. The IVT products were then column-purified, fragmented, and hybridized onto Affymetrix U133 Plus 2.0 GeneChips® at 45º C for 16 h. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin

scan_protocol: Arrays were scanned in an Affymetrix GeneChip® Scanner 3000

data_processing: Base-2 logarithm transformed intensity data from the two batches of samples were normalized within each batch using frozen robust multi-array analysis (frozen RMA).

source_name: pulmonary metastasis

label_protocol: Microarray analysis was conducted according to manufacturer’s instructions for the Affymetrix One Cycle Target Labeling and Control Reagents kit

extract_protocol: The Mayo Biospecimen Accessioning and Processing Core performed RNA extractions using kits and protocols from the Qiagen miRNEasy kit and Qiagen Qiacube instrument.

tag: patient

value: Mets

tag: primary subtype

value: ccRCC


title: 655

source_name: kidney tumor

value: Primary


title: 915


title: Day 3 Clone 5 eAPC:4-1BBL


title: 1366


title: 819


title: Day 3 Clone 3 eAPC:4-1BBL


title: Day 3 Clone 2 eAPC:4-1BBL


title: 449


title: 1363


title: 1374


title: 785


title: Day 3 Clone 4 eAPC


title: Day 3 Clone 1 eAPC:4-1BBL


title: 252


title: 1350


title: 1338


title: 1370


title: Day 7 Clone 7 eAPC


title: Day 3 Clone 1 eAPC


title: Day 3 Clone 5 eAPC


title: Day 7 Clone 6 eAPC


title: 1334


title: 131


title: 1060


title: 204


title: 1354


title: sample 6 week 0 BLCC treated

city: Miami

first: Horacio

middle: Adrian

last: Ramirez

address: 1600 NW10th Avenue RMSB room 2029A

department: Dermatology

institute: University of Miami

hyb_protocol: Hybridization was done using the GeneChip Hybridization Wash and Stain Kit

scan_protocol: Chips were scanned with a GeneChip scanner 3000 (Affymetrix)

data_processing: The 18 chronic VLU dataset files and the 14 acute wounding files were imported into Genespring 13.0 (Agilent Technologies), and were collectively normalized and summarized using the GC Robust Multi-array Average (GCRMA) algorithm. Probe sets were filtered to exclude probes not detected in the samples

source_name: week 0_BLCC treated

label_protocol: fragmentation and labeling were done using the GeneChip 3’ IVT Express kit following affymetrix protocols

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

tag: subject status

value: venous leg ulcers (VLUs) patients

tag: subject group

value: treatment group receiving weekly BLCC applications

tag: time point

value: at the time of randomization (week 0)

value: skin biopsy specimens (from the non-healing edges of VLU’s)


title: sample 6 week 1 BLCC treated

source_name: week 1_BLCC treated

value: one week later (week 1)


title: 740


title: 1358


title: 504


title: 1327


title: 223


title: sample 5 week 1 BLCC treated


title: 94


title: 1364


title: sample 3 week 0 BLCC treated


title: 1905


title: sample 2 week 1 BLCC treated


title: sample 2 week 0 BLCC treated


title: 944


title: sample 3 week 1 BLCC treated


title: sample 4 week 0 BLCC treated


title: sample 1 week 1 BLCC treated


title: Day 7 Clone 8 eAPC:4-1BBL


title: sample 4 week 1 BLCC treated


title: 1368


title: sample 5 week 0 BLCC treated


title: 1343

value: Papillary RCC


title: sample 3 week 0 contol

source_name: week 0_control

value: control group receiving standard-of-care compression therapy


title: sample 1 week 0 control


title: sample 3 week 1 control

source_name: week 1_control


title: sample 1 week 1 control


title: sample 2 week 0 control


title: sample 2 week 1 control


title: sample 1 week 0 BLCC treated


title: second_trimester_FMR1_fullmutation_male2

city: Boston

first: Lillian

last: Zwemer

state: MA

address: 800 Washington St, Box 394

department: Mother Infant Research Institute

institute: Tufts Medical Center

description: gene expression data from second trimester fetus with one full mutation length FMR1 allele

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.

source_name: cell free mRNA from second trimester amniotic fluid

label_protocol: Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)

extract_protocol: RNA was extracted from 5-15 mL amniotic fluid supernatant (centrifugation at 350g, 4C, 10, min).All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.

treatment_protocol: RNA was extracted from 5-15 mL amniotic fluid supernatant (centrifugation at 350g, 4C, 10, min). All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.

tag: gender

value: male

tag: genotype/variation

value: one full mutation length FMR1 allele


title: second_trimester_FMR1_premutation_male12

description: gene expression data from second trimester fetus with one premutation length FMR1 allele

value: one premutation length FMR1 allele


title: second_trimester_FMR1_premutation_female15

value: female


title: second_trimester_FMR1_premutation_male11


title: second_trimester_FMR1_premutation_male8


title: second_trimester_FMR1_premutation_male3


title: second_trimester_FMR1_premutation_female18


title: second_trimester_FMR1_premutation_male5


title: second_trimester_FMR1_premutation_male6


title: second_trimester_FMR1_premutation_female16


title: second_trimester_FMR1_premutation_male7


title: second_trimester_FMR1_fullmutation_female1


title: second_trimester_FMR1_premutation_female17


title: second_trimester_FMR1_premutation_male10


title: second_trimester_FMR1_premutation_male4


title: second_trimester_FMR1_normal_female18

description: gene expression data from second trimester fetus with normal length FMR1 alleles

value: normal


title: second_trimester_FMR1_normal_female17


title: second_trimester_FMR1_premutation_female13


title: second_trimester_FMR1_premutation_male1


title: second_trimester_FMR1_normal_female14


title: second_trimester_FMR1_normal_female16


title: second_trimester_FMR1_premutation_female14


title: second_trimester_FMR1_premutation_male2


title: second_trimester_FMR1_fullmutation_female2


title: second_trimester_FMR1_fullmutation_male1


title: second_trimester_FMR1_normal_female15


title: 10


title: second_trimester_FMR1_normal_female13


title: second_trimester_FMR1_normal_male9


title: second_trimester_FMR1_normal_male10


title: second_trimester_FMR1_normal_male11


title: second_trimester_FMR1_normal_male5


title: second_trimester_FMR1_normal_male12


title: second_trimester_FMR1_normal_male6


title: second_trimester_FMR1_normal_male7


title: second_trimester_FMR1_normal_male4


title: second_trimester_FMR1_normal_male1


title: Hela infected with EDL933 for 4 hours biological rep3

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

description: Gene expression data from Hela cells infected for hours with EDL933

hyb_protocol: Following labelling , 80pmoles of labelled probe was hybridized for 16 hr at 42C on Human whole genome arrays. GeneChips were washed using Adwawash.

scan_protocol: GeneChips were scanned using the Perkin-Elmer Scanarray Scanner 4200.

data_processing: The data were analyzed with Scanarray express microarray analysis system and quantile normalization was used in R package to normalise the data.

label_protocol: Labelled cDNA was hybridised on Human custom made arrays.

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

tag: Hela cell wildtype

tag: 4 hour post infection


title: second_trimester_FMR1_normal_male3


title: CaCo2 infected with shocked and unshocked EDL rep2

description: Gene expression data from CaCo2 cells infected with shocked(cy5) and unshocked(cy3) bacteria double channel arrays

source_name: CaCo2 cells infected with acid-shocked bacteria

tag: CaCo2 cells 4 hour post infection

tag: CaCo2 cell wildtype

source_name: CaCo2 cells infected with unshocked bacteria


title: Hela infected with EDL933 for 4 hours biological rep1

source_name: Hela cells infected for hours with EDL933


title: CaCo2 infected with EPEC for 4 hours biological rep1

description: Gene expression data from CaCo2 cells infected for hours with EPEC


title: CaCo2 infected with EDL933 for 4 hours biological rep3

description: Gene expression data from CaCo2 cells infected for hours with EDL933


title: Hela uninfected 4 hours biological rep1

description: Gene expression data from Hela cells uninfected control

source_name: Hela cells uninfected control


title: second_trimester_FMR1_normal_male2


title: Hela uninfected 4 hours biological rep3


title: Hela infected with EDL933 for 4 hours biological rep2


title: CaCo2 infected with shocked and unshocked EDL rep3


title: second_trimester_FMR1_normal_male8


title: CaCo2 infected with shocked and unshocked EDL rep1


title: Hela uninfected 4 hours biological rep2


title: CaCo2 uninfected 4 hours biological rep3

description: Gene expression data from CaCo2 cells uninfected control

source_name: CaCo2 cells uninfected control


title: CaCo2 infected with EDL933 for 4 hours biological rep1

source_name: CaCo2 cells infected for hours with EDL933


title: CaCo2 infected with EPEC for 4 hours biological rep2

source_name: CaCo2 cells infected for hours with EPEC


title: CaCo2 infected with EDL933 for 4 hours biological rep2


title: CaCo2 uninfected 4 hours biological rep2


title: CaCo2 uninfected 4 hours biological rep1


title: 1341

tag: tissue


title: second_trimester_FMR1_premutation_male9


title: AML 5074 (CD33/CD14neg)

city: Leiden

first: Marieke

last: Griffioen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized in R

source_name: Acute myeloid leukemia cells isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and lack of CD14 surface expression

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amp kit for Illumina arrays

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

value: peripheral blood

value: Acute myeloid leukemia cells

tag: protocol


title: ALL 1299 (CD19)

source_name: Acute lymphoblastic leukemia cells isolated from samples with >85% leukemic blasts (range 85-98%) based on CD19 surface expression

value: bone marrow

value: Acute lymphoblastic leukemia cells


title: AML 5074 (CD33/CD14pos)

source_name: Acute myeloid leukemia cells isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and CD14 surface expression


title: AML 5596 (CD33)

source_name: Acute myeloid leukemia cells isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 surface expression


title: ALL 3639 (CD19)

value: isolated from samples with >85% leukemic blasts (range 85-98%) based on CD19 surface expression


title: ALL 3655 (CD19)


title: AML 3590 (CD33)

value: isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 surface expression


title: AML 4781 (CD33/CD14neg)

value: isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and lack of CD14 surface expression


title: AML 1310 (CD33/CD14pos)

value: isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and CD14 surface expression


title: AML 5205 (CD33/CD14neg)


title: CML 1303 (CD34)

source_name: Chronic myeloid leukemia cells isolated from samples with >5% hematopoietic progenitor cells based on CD34 surface expression

value: Chronic myeloid leukemia cells


title: AML 1310 (CD33/CD14neg)


title: FB 3087B + IFN-γ

source_name: Fibroblasts cultured from a skin derived biopsy in DMEM with low glucose, cultured with IFN-γ

value: skin

value: Fibroblasts


title: AML 4443 (CD33)


title: AML 5205 (CD33/CD14pos)


title: FB 3087B

source_name: Fibroblasts cultured from a skin derived biopsy in DMEM with low glucose


title: Melanocytes 8018 + IFN-γ

source_name: Melanocytes cultured from surgically removed nevi in F10 supplemented medium and IFN-γ (100 IU/mL) for 4 days

value: Melanocytes


title: matDC 3087

source_name: Mature dendritic cells cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days. TNF-α, IL-1β, IL-6, prostaglandin E2 and IFN-γ was added during the final 2 days for maturation.

value: Mature dendritic cells


title: HSC 5321 (CD34)

source_name: Hematopoietic stem cells isolated by flowcytometry based on CD34 surface expression

value: G-CSF mobilized peripheral blood

value: Hematopoietic stem cells

value: isolated by flow cytometry based on CD34 surface expression


title: mono 3087 (CD14)

source_name: Monocytes isolated by flowcytometry based on CD14 surface expression

value: Monocytes

value: isolated by flow cytometry based on CD14 surface expression


title: imDC 3087

source_name: Immature dendritic cells cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days

value: peripheral blood

value: Immature dendritic cells


title: KC 4769 + IFN-γ

source_name: Keratinocytes cultured from a skin derived biopsy in DMEM with low glucose and IFN-γ (100 IU/mL) for 4 days

value: Keratinocytes


title: EBV-B 3087C

source_name: B-cells immortalized by Epstein Barr Virus

value: B-cells

value: immortalized by Epstein Barr Virus


title: KC 6342 + IFN-γ

value: cultured from a skin derived biopsy in DMEM with low glucose and IFN-γ (100 IU/mL) for 4 days


title: Melanocytes 8018

source_name: Melanocytes cultured from surgically removed nevi in F10 supplemented medium


title: AML 3870 (CD33)

value: bone marrow

value: Acute myeloid leukemia cells

value: isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 surface expression


title: HSC 5381 (CD34)


title: ALL 2391 (CD19)

value: Acute lymphoblastic leukemia cells

value: isolated from samples with >85% leukemic blasts (range 85-98%) based on CD19 surface expression


title: T-cells 3087 (CD3)

source_name: T-cells isolated by flowcytometry based on CD3 surface expression

value: T-cells

value: isolated by flow cytometry based on CD3 surface expression


title: PBMC 3087

source_name: Mononuclear cells isolated from peripheral blood after Ficoll-Isopaque separation

value: Mononuclear cells


title: AML 6283 (CD33)


title: AML 3778 (CD33)


title: ALL 1833 (CD19)


title: FB 7645 + IFN-γ

source_name: Fibroblasts cultured from a skin derived biopsy in DMEM with low glucose, cultured with IFN-γ for 4 days

value: skin

value: Fibroblasts


title: AML 1466 (CD33/CD14pos)

value: isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and CD14 surface expression


title: ALL 2375 (CD19)

source_name: Acute lymphoblastic leukemia cells isolated from samples with >85% leukemic blasts (range 85-98%) based on CD19 surface expression


title: ALL 2872 (CD19)


title: Melanocytes 1912

value: Melanocytes

value: cultured from surgically removed nevi in F10 supplemented medium


title: ALL 5903 (CD19)


title: HELA TK-

source_name: Cell line from human cervix adenocarcinoma

value: cervix

tag: cell line

value: HELA TK-


title: FB 7645

value: cultured from a skin derived biopsy in DMEM with low glucose


title: CML 3087 (CD34)

value: Chronic myeloid leukemia cells

value: isolated from samples with >5% hematopoietic progenitor cells based on CD34 surface expression


title: AML 1466 (CD33/CD14neg)

source_name: Acute myeloid leukemia cells isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and lack of CD14 surface expression

value: bone marrow

value: Acute myeloid leukemia cells


title: HSC 5000 (CD34)

value: G-CSF mobilized peripheral blood

value: Hematopoietic stem cells

value: isolated by flow cytometry based on CD34 surface expression


title: AML 2467 (CD33/CD14pos)

source_name: Acute myeloid leukemia cells isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and CD14 surface expression

value: peripheral blood


title: PTEC 03

source_name: Proximal tubular epithelial cells cultured in serum-free DMEM/HAM-F12 with insulin, transferrin, selenium, triiodothyronine, epidermal growth factor and hydrocortisone

value: kidney

value: Proximal tubular epithelial cells


title: EBV-B 3089D

value: B-cells

value: immortalized by Epstein Barr Virus


title: PTEC 03 + IFN-γ

source_name: Proximal tubular epithelial cells cultured in serum-free DMEM/HAM-F12 with insulin, transferrin, selenium, triiodothyronine, epidermal growth factor and hydrocortisone and IFN-γ (100 IU/mL) for 4 days


title: PTEC 02 + IFN-γ

value: cultured in serum-free DMEM/HAM-F12 with insulin, transferrin, selenium, triiodothyronine, epidermal growth factor and hydrocortisone and IFN-γ (100 IU/mL) for 4 days


title: AML 2467 (CD33/CD14neg)

value: isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and lack of CD14 surface expression


title: B-cells 5000 (CD19)

source_name: B-cells isolated by flowcytometry based on CD19 surface expression

value: isolated by flow cytometry based on CD19 surface expression


title: Melanocytes 1912 + IFN-γ

source_name: Melanocytes cultured from surgically removed nevi in F10 supplemented medium and IFN-γ (100 IU/mL) for 4 days

value: skin

value: Melanocytes


title: Melanocytes 0223

value: cultured from surgically removed nevi in F10 supplemented medium


title: KC 4769

source_name: Keratinocytes cultured from a skin derived biopsy in DMEM with low glucose

value: Keratinocytes


title: KC 6342

value: cultured from a skin derived biopsy in DMEM with low glucose


title: mono 4762 (CD14)

source_name: Monocytes isolated by flowcytometry based on CD14 surface expression

value: Monocytes

value: isolated by flow cytometry based on CD14 surface expression


title: matDC 4762

source_name: Mature dendritic cells cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days. TNF-α, IL-1β, IL-6, prostaglandin E2 and IFN-γ was added during the final 2 days for maturation.

value: Mature dendritic cells


title: Melanocytes 0223 + IFN-γ

value: cultured from surgically removed nevi in F10 supplemented medium and IFN-γ (100 IU/mL) for 4 days


title: EBV-B 3089C

value: peripheral blood


title: PTEC 02

value: kidney

value: cultured in serum-free DMEM/HAM-F12 with insulin, transferrin, selenium, triiodothyronine, epidermal growth factor and hydrocortisone


title: KC 6317


title: FB 5852A + IFN-γ

value: Fibroblasts

value: cultured from a skin derived biopsy in DMEM with low glucose, cultured with IFN-γ for 4 days


title: KC 6317 + IFN-γ

source_name: Keratinocytes cultured from a skin derived biopsy in DMEM with low glucose and IFN-γ (100 IU/mL) for 4 days


title: imDC 4762

source_name: Immature dendritic cells cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days

value: Immature dendritic cells


title: T-cells 4762 (CD3)

value: T-cells

value: isolated by flow cytometry based on CD3 surface expression


title: B-cells 4762 (CD19)

value: B-cells

value: isolated by flow cytometry based on CD19 surface expression


title: EBV-B 3089B

source_name: B-cells immortalized by Epstein Barr Virus

value: immortalized by Epstein Barr Virus


title: FB 5852A

source_name: Fibroblasts cultured from a skin derived biopsy in DMEM with low glucose

value: skin


title: 7_HOXA9+MEIS1 w4 #1 L

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Expression Console software. Probe intensities, gene level expression were RMA summarized and then quantile normalized.
MoEx-1_0-st-v1.r2.pgf'
MoEx-1_0-st-v1.r2.mps
Quantile normalized gene level expression values from Expression Console software

organism: Mus musculus

source_name: Mouse cell culture

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

tag: strain

tag: Sex

value: Female

tag: age

value: Cells from 12 week old 5-FU treated mice

value: Bone marrow

tag: developmental stage

value: Progenitor cells

value: Primary bone marrow culture

tag: genetic modification

value: Transduced with MSCV construct

tag: genetic characteristics

value: Overexpression of HOXA9 and MEIS1

tag: growth condition

value: DMEM 15% FCS, IL3, SCF, IL6


title: PTEC 01 + IFN-γ

value: kidney

tag: cell type

value: Proximal tubular epithelial cells

value: cultured in serum-free DMEM/HAM-F12 with insulin, transferrin, selenium, triiodothyronine, epidermal growth factor and hydrocortisone and IFN-γ (100 IU/mL) for 4 days


title: 10_HOXA9+MDHD w3 #2 L

value: Overexpression of HOXA9 and MEIS1dHD


title: 12_HOXA9+MDHD w4 #2 L


title: CML 4779 (CD34)

source_name: Chronic myeloid leukemia cells isolated from samples with >5% hematopoietic progenitor cells based on CD34 surface expression

value: bone marrow

value: Chronic myeloid leukemia cells


title: 5_HOXA9+MEIS1 w3 #1 L


title: T-cells 5957 (CD3)

source_name: T-cells isolated by flowcytometry based on CD3 surface expression

value: peripheral blood

value: T-cells

value: isolated by flow cytometry based on CD3 surface expression


title: PTEC 01

value: cultured in serum-free DMEM/HAM-F12 with insulin, transferrin, selenium, triiodothyronine, epidermal growth factor and hydrocortisone


title: mono 5957 (CD14)

value: Monocytes

value: isolated by flow cytometry based on CD14 surface expression


title: EBV-B 3087B

value: B-cells

value: immortalized by Epstein Barr Virus


title: matDC 5957

source_name: mature dendritic cells cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days. TNF-α, IL-1β, IL-6, prostaglandin E2 and IFN-γ was added during the final 2 days for maturation.

value: mature dendritic cells


title: PBMC 4762

source_name: Mononuclear cells isolated from peripheral blood after Ficoll-Isopaque separation

value: Mononuclear cells


title: PBMC 5957

value: isolated from peripheral blood after Ficoll-Isopaque separation


title: FB 4766A

value: skin

value: Fibroblasts

value: cultured from a skin derived biopsy in DMEM with low glucose


title: FB 4766A + IFN-γ

source_name: Fibroblasts cultured from a skin derived biopsy in DMEM with low glucose, cultured with IFN-γ for 4 days


title: imDC 5957

value: Immature dendritic cells

value: cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days


title: B-cells 5957 (CD19)

value: isolated by flow cytometry based on CD19 surface expression


title: CML 2195 (CD34)

source_name: Juvenile myelomonocytic leukemia (JMML) formerly referred to as juvenile chronic myeloid leukemia

value: bone marrow


title: 2_HOXA9+MIY w3 #2 L

value: Female

value: Cells from 12 week old 5-FU treated mice

value: Bone marrow

value: Progenitor cells

value: Primary bone marrow culture

value: Transduced with MSCV construct

value: Overexpression of HOXA9

value: DMEM 15% FCS, IL3, SCF, IL6


title: AML 2179 (CD33)

source_name: Acute myeloid leukemia cells isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 surface expression

value: peripheral blood

value: Acute myeloid leukemia cells


title: 3_HOXA9+MIY w4 #1 L


title: 8_HOXA9+MEIS1 w4 #2 L

value: Overexpression of HOXA9 and MEIS1


title: CML 3471 (CD34)

value: Chronic myeloid leukemia cells

value: isolated from samples with >5% hematopoietic progenitor cells based on CD34 surface expression


title: 6_HOXA9+MEIS1 w3 #2 L


title: 11_HOXA9+MDHD w4 #1 L

value: Overexpression of HOXA9 and MEIS1dHD


title: 4_HOXA9+MIY w4 #2 L


title: AML 3714 (CD33)

value: isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 surface expression


title: FB 3087A

value: skin

value: Fibroblasts

value: cultured from a skin derived biopsy in DMEM with low glucose


title: PHA-T 3087

source_name: PHA-T blasts generated by stimulating PBMC with IL-2 and PHA

value: PHA-T blasts


title: AML 3370 (CD33)


title: EBV-B 3087A

value: B-cells

value: immortalized by Epstein Barr Virus


title: EBV-B 2877


title: PHA-T 2877A

value: generated by stimulating PBMC with IL-2 and PHA


title: EBV-B 2876


title: ALL 3281 (CD19)

source_name: Acute lymphoblastic leukemia cells isolated from samples with >85% leukemic blasts (range 85-98%) based on CD19 surface expression

value: Acute lymphoblastic leukemia cells


title: EBV-B 5852


title: CML 5036 (CD34)


title: 9_HOXA9+MDHD w3 #1 L

value: Female

value: Cells from 12 week old 5-FU treated mice

value: Bone marrow

value: Progenitor cells

value: Primary bone marrow culture

value: Transduced with MSCV construct


title: 1_HOXA9+MIY w3 #1 L

value: Overexpression of HOXA9

value: DMEM 15% FCS, IL3, SCF, IL6


title: LNCaP empty vector control-replicate 4

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

description: Replicate 4

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

source_name: LNCaP cell line transiently transfected with empty vector- Day 4 post transfection (control)

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

growth_protocol: PNT1a and LNCaP cells were cultured in RPMI supplemented with 10% FBS. PNT1a stable lines were maintained in 0.8 mg/ml G418 supplemented Media.

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

value: LNCaP prostate cancer cell line


title: LNCaP transiently overexpressing HIP1-replicate 6

description: Replicate 6

source_name: LNCaP cell line transiently overexpressing HIP1- Day 4 post transfection


title: PHA-T 5852

value: peripheral blood


title: LNCaP transiently overexpressing HIP1-replicate 1

description: Replicate 1


title: LNCaP transiently overexpressing HIP1-replicate 2

description: Replicate 2


title: LNCaP empty vector control-replicate 2

description: Replicate 2


title: LNCaP empty vector control-replicate 6

description: Replicate 6


title: PNT1a stably overexpressing HIP1-Replicate 6

description: Replicate 6

source_name: PNT1a cell line stably overexpressing HIP1

value: PNT1a- immortalised prostate epithelial cell line


title: LNCaP transiently overexpressing HIP1- replicate 4

description: Replicate 4


title: LNCaP empty vector control-replicate 1

description: Replicate 1


title: PNT1a stably overexpressing HIP1-Replicate 4

description: Replicate 4


title: LNCaP transiently overexpressing HIP1-replicate 5

description: Replicate 5


title: LNCaP empty vector control-replicate 3

description: Replicate 3


title: EBV-B 3089A


title: LNCaP empty vector control-replicate 5

description: Replicate 5


title: PNT1a stably overexpressing HIP1-Replicate 5

description: Replicate 5


title: LNCaP transiently overexpressing HIP1- Replicate 3

description: Replicate 3


title: Rap1 Mock ChIP Meiosis TC - Meiosis 12 hours Replicate 4

type: genomic

city: Chicago

first: Sean

middle: Erik

last: Hanlon

state: IL

address: 920 E. 58th Street – CLSC 515E

department: Department of Human Genetics

institute: University of Chicago

description: Rap1 binding dynamics during meiosis timecourse. Mock Rap1 ChIP meiosis (sporulation) 12 hour sample.

hyb_protocol: Labeled ChIP and input samples were competitively hybridized to yeast whole genome PCR based spotted arrays (resolution ~1kb). Briefly, labeled DNA, 4X SSC, and 0.2% SDS were combined and heated to 100C for 2 minutes and then cooled to 25C. The hybridization mixture was applied to the arrays and hybridizations were carried out overnight at 65C.

scan_protocol: The arrays were scanned with an Axon 4000B scanner, and data was extracted using GenePix 6.0 software.

data_processing: Probes of poor quality by visual inspection, with more than 10% saturated pixels in either channel, with a background corrected sum of medians for both channels less than 500, or with fewer than 40 foreground pixels were excluded from analysis (flagged as bad in GenePix). Additionally, failed probes and probes representing the mitochondrial genome were excluded. For the remaining probes, the median of the ratios (ChIP/Input) for each probe was converted to a log2 ratio. These log2 ratios (ChIP/Input) were then converted to z scores by centering at a mean of zero and scaling the standard deviation to one.

molecule: genomic DNA

organism: Saccharomyces cerevisiae SK1

source_name: Mock Rap1 ChIP DNA from Meiosis 12 hours

label_protocol: ChIP enriched and input DNA were amplified and labeled using Round A/B/C amplification incorporating Cy3 or Cy5 conjugated dUTP (Amersham) as before (Lieb et al., Nat Genet. 2001 Aug;28(4):327-34).

growth_protocol: Vegetative cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6-0.8 and 100 ml of cells were collected. Synchronous meiosis/sporulation was carried out by using YPD overnight cultures to inoculate YPA (1% yeast extract, 2% peptone, 2% potassium acetate) cultures at an OD600 of 0.1. YPA cultures were grown at 30C to an OD600 of 0.8-1.2 (about 16 hours). Cells were collected by centrifugation and washed with SM (2% potassium acetate). The cells were resuspended at an OD600 of 2.0 in SM (~600ml) and incubated in 2L flasks at 30C with shaking at 265 rpm. Cells were collected after 8 hours in YPA media (150 ml of cells) and after 0, 1.5, 3, 4.5, 6, 9 or 12 hours in SM (50 ml of cells). All samples were fixed with 1% formaldehyde for 20 minutes at room temperature and washed twice with 1X cold PBS. Samples were then snap frozen in a dry ice/ethanol bath and stored at -80C until ChIPs were performed.

extract_protocol: ChIPs were performed as before (Lieb et al., Nat Genet. 2001 Aug;28(4):327-34) with minor modifications. Briefly, 1% formaldehyde-fixed cells were resuspended in lysis buffer (50 mM Hepes-KOH, pH 7.5, 10 mM MgCl2, 150 mM KCl, 0.1 mM EDTA, 10% Glycerol, 0.1 % NP 40, and 1 X protease inhibitors (Calbiochem)) and disrupted using a Mini-Beadbeater-8. The isolated chromatin was sheared to an average size of 0.8 kb and incubated overnight at 4C with antibodies against Rap1 amino acids 528-827 from Santa-Cruz Biotechnology (Rap1 Y-300: sc-20167), or with no antibody for mock ChIPs. Antibody-protein-DNA complexes were recovered by incubation with Protein G Sepharose beads in IP Buffer (25 mM Hepes-KOH pH 7.5, 12.5 mM MgCl2, 150 mM KCl, 1 mM EDTA and 0.1% NP40) for 2 hours at 4C. The beads were washed four times with IP Buffer, IP Elution Buffer (50 mM Tris-Cl pH 8.0, 10 mM EDTA, 1% SDS) was added to the washed beads and Rap1 associated DNA fragments were eluted by incubation for 1 hour at 65C. Eluted ChIP samples (and inputs) were incubated at 65C overnight to reverse cross-links, excess protein was degraded using Proteinase K and DNA was isolated using Zymo columns according to the manufacturer’s instructions (Zymo Research).

value: SK1 yeast strain SHy002

value: Meiosis 12 hours

tag: molecule

value: Mock Rap1 ChIP DNA

tag: antibody

tag: antibody dilution

source_name: Input DNA from Meiosis 12 hours

value: Input DNA


title: Rap1 Mock ChIP Meiosis TC - Meiosis 6 hours Replicate 4

description: Rap1 binding dynamics during meiosis timecourse. Mock Rap1 ChIP meiosis (sporulation) 4.5 hour sample.

source_name: Mock Rap1 ChIP DNA from Meiosis 6 hours

value: Meiosis 6 hours

source_name: Input DNA from Meiosis 6 hours


title: Rap1 Mock ChIP Meiosis TC - Meiosis 12 hours Replicate 3


title: Rap1 Mock ChIP Meiosis TC - Meiosis 9 hours Replicate 3

description: Rap1 binding dynamics during meiosis timecourse. Mock Rap1 ChIP meiosis (sporulation) 6 hour sample.

source_name: Input DNA from Meiosis 9 hours

value: Meiosis 9 hours

source_name: Mock Rap1 ChIP DNA from Meiosis 9 hours


title: PNT1a empty vector control-replicate 4

description: Replicate 4

source_name: PNT1a cell line stably transfected with empty vector (control)


title: Rap1 Mock ChIP Meiosis TC - Meiosis 3 hours Replicate 4

description: Rap1 binding dynamics during meiosis timecourse. Mock Rap1 ChIP meiosis (sporulation) 3 hour sample.

source_name: Mock Rap1 ChIP DNA from Meiosis 3 hours

value: Meiosis 3 hours

source_name: Input DNA from Meiosis 3 hours


title: PNT1a empty vector control-replicate 6

description: Replicate 6


title: PNT1a empty vector control-replicate 2

description: Replicate 2


title: PNT1a stably overexpressing HIP1-Replicate 1

description: Replicate 1


title: PNT1a empty vector control-replicate 1

description: Replicate 1


title: PNT1a empty vector control-replicate 5

description: Replicate 5


title: Rap1 Mock ChIP Meiosis TC - Meiosis 6 hours Replicate 3


title: PNT1a stably overexpressing HIP1-Replicate 3

description: Replicate 3


title: Rap1 Mock ChIP Meiosis TC - Meiosis 3 hours Replicate 3


title: PNT1a stably overexpressing HIP1-Replicate 2

description: Replicate 2


title: Rap1 Mock ChIP Meiosis TC - Meiosis 1.5 hours Replicate 4

description: Rap1 binding dynamics during meiosis timecourse. Mock Rap1 ChIP meiosis (sporulation) 1.5 hour sample.

source_name: Mock Rap1 ChIP DNA from Meiosis 1.5 hours

value: Meiosis 1.5 hours

source_name: Input DNA from Meiosis 1.5 hours


title: Rap1 Mock ChIP Meiosis TC - YPA 8 hours Replicate 3

description: Rap1 binding dynamics during meiosis timecourse. Mock Rap1 ChIP YPA (respiratory) growth sample.

source_name: Input DNA from YPA 8 hours

value: YPA 8 hours

source_name: Mock Rap1 ChIP DNA from YPA 8 hours


title: Rap1 Mock ChIP Meiosis TC - Meiosis 1.5 hours Replicate 3


title: Rap1 Mock ChIP Meiosis TC - YPA 8 hours Replicate 4


title: Rap1 Mock ChIP Meiosis TC - Meiosis 4.5 hours Replicate 4

source_name: Mock Rap1 ChIP DNA from Meiosis 4.5 hours

value: Meiosis 4.5 hours

source_name: Input DNA from Meiosis 4.5 hours


title: PNT1a empty vector control-replicate 3

description: Replicate 3


title: Rap1 Mock ChIP Meiosis TC - Meiosis 0 hours Replicate 3

description: Rap1 binding dynamics during meiosis timecourse. Mock Rap1 ChIP meiosis (sporulation) 0 hour sample.

source_name: Input DNA from Meiosis 0 hours

value: Meiosis 0 hours

source_name: Mock Rap1 ChIP DNA from Meiosis 0 hours


title: Rap1 Mock ChIP Meiosis TC - YPD Replicate 4

description: Rap1 binding dynamics during meiosis timecourse. Mock Rap1 ChIP YPD (logarithmic) growth sample.

source_name: Mock Rap1 ChIP DNA from YPD

value: YPD

source_name: Input DNA from YPD


title: Rap1 Mock ChIP Meiosis TC - Meiosis 0 hours Replicate 4


title: Rap1 Mock ChIP Meiosis TC - YPD Replicate 3


title: Rap1 ChIP Meiosis TC - Meiosis 12hrs Replicate 7

description: Rap1 binding dynamics during meiosis timecourse. Rap1 ChIP meiosis (sporulation) 12 hour sample.

source_name: Input DNA from Meiosis 12 hours

source_name: Rap1 ChIP DNA from Meiosis 12 hours

value: Rap1 ChIP DNA

value: anti-Rap1 y300


title: Rap1 ChIP Meiosis TC - Meiosis 12hrs Replicate 5


title: Rap1 Mock ChIP Meiosis TC - Meiosis 9 hours Replicate 4

source_name: Input DNA from Meiosis 9 hours


title: Rap1 ChIP Meiosis TC - Meiosis 12hrs Replicate 6


title: Rap1 Mock ChIP Meiosis TC - Meiosis 4.5 hours Replicate 3


title: Rap1 ChIP Meiosis TC - Meiosis 9hrs Replicate 7

description: Rap1 binding dynamics during meiosis timecourse. Rap1 ChIP meiosis (sporulation) 9 hour sample.

source_name: Rap1 ChIP DNA from Meiosis 9 hours


title: Rap1 ChIP Meiosis TC - Meiosis 12hrs Replicate 2


title: Rap1 ChIP Meiosis TC - Meiosis 12hrs Replicate 4


title: Rap1 ChIP Meiosis TC - Meiosis 12hrs Replicate 3


title: Rap1 ChIP Meiosis TC - Meiosis 12hrs Replicate 1


title: Rap1 ChIP Meiosis TC - Meiosis 9hrs Replicate 4


title: Rap1 ChIP Meiosis TC - Meiosis 9hrs Replicate 2


title: Rap1 ChIP Meiosis TC - Meiosis 9hrs Replicate 1


title: Rap1 ChIP Meiosis TC - Meiosis 9hrs Replicate 6


title: Rap1 ChIP Meiosis TC - Meiosis 6hrs Replicate 7

description: Rap1 binding dynamics during meiosis timecourse. Rap1 ChIP meiosis (sporulation) 6 hour sample.

source_name: Input DNA from Meiosis 6 hours

source_name: Rap1 ChIP DNA from Meiosis 6 hours


title: Rap1 ChIP Meiosis TC - Meiosis 6hrs Replicate 5


title: Rap1 ChIP Meiosis TC - Meiosis 6hrs Replicate 6


title: Rap1 ChIP Meiosis TC - Meiosis 6hrs Replicate 4


title: Rap1 ChIP Meiosis TC - Meiosis 4.5hrs Replicate 6

description: Rap1 binding dynamics during meiosis timecourse. Rap1 ChIP meiosis (sporulation) 4.5 hour sample.

source_name: Rap1 ChIP DNA from Meiosis 4.5 hours


title: Rap1 ChIP Meiosis TC - Meiosis 9hrs Replicate 3


title: Rap1 ChIP Meiosis TC - Meiosis 4.5hrs Replicate 5


title: Rap1 ChIP Meiosis TC - Meiosis 4.5hrs Replicate 1


title: Rap1 ChIP Meiosis TC - Meiosis 3hrs Replicate 7

description: Rap1 binding dynamics during meiosis timecourse. Rap1 ChIP meiosis (sporulation) 3 hour sample.

source_name: Input DNA from Meiosis 3 hours

source_name: Rap1 ChIP DNA from Meiosis 3 hours


title: Rap1 ChIP Meiosis TC - Meiosis 6hrs Replicate 3


title: Rap1 ChIP Meiosis TC - Meiosis 9hrs Replicate 5


title: Rap1 ChIP Meiosis TC - Meiosis 3hrs Replicate 5


title: Rap1 ChIP Meiosis TC - Meiosis 4.5hrs Replicate 3


title: Rap1 ChIP Meiosis TC - Meiosis 3hrs Replicate 3


title: Rap1 ChIP Meiosis TC - Meiosis 3hrs Replicate 6


title: Rap1 ChIP Meiosis TC - Meiosis 6hrs Replicate 1


title: Rap1 ChIP Meiosis TC - Meiosis 6hrs Replicate 2


title: Rap1 ChIP Meiosis TC - Meiosis 3hrs Replicate 4


title: Rap1 ChIP Meiosis TC - Meiosis 4.5hrs Replicate 4


title: Rap1 ChIP Meiosis TC - Meiosis 3hrs Replicate 2


title: Rap1 ChIP Meiosis TC - Meiosis 3hrs Replicate 1


title: Rap1 ChIP Meiosis TC - Meiosis 1.5hrs Replicate 4

description: Rap1 binding dynamics during meiosis timecourse. Rap1 ChIP meiosis (sporulation) 1.5 hour sample.

source_name: Rap1 ChIP DNA from Meiosis 1.5 hours

source_name: Input DNA from Meiosis 1.5 hours


title: Rap1 ChIP Meiosis TC - Meiosis 1.5hrs Replicate 7


title: Rap1 ChIP Meiosis TC - Meiosis 1.5hrs Replicate 2


title: Rap1 ChIP Meiosis TC - Meiosis 1.5hrs Replicate 1


title: Rap1 ChIP Meiosis TC - Meiosis 4.5hrs Replicate 7


title: Rap1 ChIP Meiosis TC - Meiosis 0hrs Replicate 7

description: Rap1 binding dynamics during meiosis timecourse. Rap1 ChIP meiosis (sporulation) 0 hour sample.

source_name: Rap1 ChIP DNA from Meiosis 0 hours


title: Rap1 ChIP Meiosis TC - Meiosis 1.5hrs Replicate 6


title: Rap1 ChIP Meiosis TC - Meiosis 0hrs Replicate 6


title: Rap1 ChIP Meiosis TC - Meiosis 0hrs Replicate 3


title: Rap1 ChIP Meiosis TC - Meiosis 0hrs Replicate 4


title: Rap1 ChIP Meiosis TC - Meiosis 0hrs Replicate 5


title: Rap1 ChIP Meiosis TC - YPD Replicate 4

description: Rap1 binding dynamics during meiosis timecourse. Rap1 ChIP YPD (logarithmic) growth sample.

source_name: Rap1 ChIP DNA from YPD


title: Rap1 ChIP Meiosis TC - Meiosis 0hrs Replicate 1

source_name: Input DNA from Meiosis 0 hours


title: Rap1 ChIP Meiosis TC - YPA 8hrs Replicate 6

description: Rap1 binding dynamics during meiosis timecourse. Rap1 ChIP YPA (respiratory) growth sample.

source_name: Rap1 ChIP DNA from YPA 8 hours

source_name: Input DNA from YPA 8 hours


title: Rap1 ChIP Meiosis TC - Meiosis 0hrs Replicate 2


title: Rap1 ChIP Meiosis TC - YPA 8hrs Replicate 7


title: Rap1 ChIP Meiosis TC - YPA 8hrs Replicate 3


title: Rap1 ChIP Meiosis TC - YPD Replicate 1

source_name: Input DNA from YPD


title: Rap1 ChIP Meiosis TC - Meiosis 1.5hrs Replicate 5


title: Rap1 ChIP Meiosis TC - YPD Replicate 5


title: Rap1 ChIP Meiosis TC - YPA 8hrs Replicate 5


title: Rap1 ChIP Meiosis TC - YPA 8hrs Replicate 2


title: Rap1 ChIP Meiosis TC - YPA 8hrs Replicate 4


title: Rap1-depletion Rap1 ChIP - YPA 20hrs Replicate 6

description: Comparing Rap1 binding by ChIP in cells with wildtype Rap1 levels and cells depleted of Rap1. YPA (respiratory growth) sample.

hyb_protocol: Labeled ChIP enriched DNA from Rap1 depeleted and non-depleted samples were competitively hybridized to yeast whole genome PCR based spotted arrays (resolution ~1kb). Briefly, labeled DNA, 4X SSC, and 0.2% SDS were combined and heated to 100C for 2 minutes and then cooled to 25C. The hybridization mixture was applied to the arrays and hybridizations were carried out overnight at 65C.

data_processing: Probes of poor quality by visual inspection, with more than 10% saturated pixels in either channel, with a background corrected sum of medians for both channels less than 500, or with fewer than 40 foreground pixels were excluded from analysis (flagged as bad in GenePix). Additionally, failed probes and probes representing the mitochondrial genome were excluded. For the remaining probes, the median of the ratios (Cy5/Cy3) for each probe was converted to a log2 ratio. These log2 ratios (Cy5/Cy3) were then converted to z scores by centering at a mean of zero and scaling the standard deviation to one.

source_name: Rap1 ChIP DNA from YPA 20 hours; Rap1 depleted

label_protocol: ChIP enriched DNA was amplified and labeled using Round A/B/C amplification incorporating Cy3 or Cy5 conjugated dUTP (Amersham) as before (Lieb et al., Nat Genet. 2001 Aug;28(4):327-34).

extract_protocol: ChIPs were performed as before (Lieb et al., Nat Genet. 2001 Aug;28(4):327-34) with minor modifications. Briefly, 1% formaldehyde-fixed cells were resuspended in lysis buffer (50 mM Hepes-KOH, pH 7.5, 10 mM MgCl2, 150 mM KCl, 0.1 mM EDTA, 10% Glycerol, 0.1 % NP 40, and 1 X protease inhibitors (Calbiochem)) and disrupted using a Mini-Beadbeater-8. The isolated chromatin was sheared to an average size of 0.8 kb and incubated overnight at 4C with antibodies against Rap1 amino acids 528-827 from Santa-Cruz Biotechnology (Rap1 Y-300: sc-20167), or with no antibody for mock ChIPs. Antibody-protein-DNA complexes were recovered by incubation with Protein G Sepharose beads in IP Buffer (25 mM Hepes-KOH pH 7.5, 12.5 mM MgCl2, 150 mM KCl, 1 mM EDTA and 0.1% NP40) for 2 hours at 4C. The beads were washed four times with IP Buffer, IP Elution Buffer (50 mM Tris-Cl pH 8.0, 10 mM EDTA, 1% SDS) was added to the washed beads and Rap1 associated DNA fragments were eluted by incubation for 1 hour at 65C. Eluted ChIP samples were incubated at 65C overnight to reverse cross-links, excess protein was degraded using Proteinase K and DNA was isolated using Zymo columns according to the manufacturer’s instructions (Zymo Research).

treatment_protocol: 50 ug/ml doxycycline

value: SHy20 (tetO7-TATA-Rap1)

value: YPA 20 hours

tag: treatment status

value: Plus doxycycline (Rap1 depleted)

value: Minus doxycycline (Rap1 on)

source_name: Rap1 ChIP DNA from YPA 20 hours

treatment_protocol: 0.33 ug/ml doxycycline


title: Rap1 ChIP Meiosis TC - YPD Replicate 2

value: SK1 yeast strain SHy002


title: Rap1 ChIP Meiosis TC - YPD Replicate 3


title: Rap1 ChIP Meiosis TC - YPD Replicate 7


title: Rap1 ChIP Meiosis TC - YPD Replicate 6


title: Rap1-depletion Rap1 ChIP - YPA 20hrs Replicate 4


title: Rap1 ChIP Meiosis TC - YPA 8hrs Replicate 1


title: Rap1-depletion Rap1 ChIP - YPA 20hrs Replicate 5


title: Rap1-depletion-Expression Meiosis TC - Meiosis 9hrs Replicate 5

description: Comparing RNA expression dynamics during meiosis timecourse in cells with wildtype Rap1 levels and cells depleted of Rap1. Meiosis (sporulation) 9 hour sample.

hyb_protocol: Labeled reverse transcribed total RNA from Rap1 depeleted and non-depleted samples at each time point were competitively hybridized to yeast whole genome PCR based spotted arrays (resolution ~1kb). Hybridizations were carried out overnight at 65 C.

data_processing: Probes of poor quality by visual inspection, with more than 10% saturated pixels in either channel, with a background corrected sum of medians for both channels less than 500, or with fewer than 40 foreground pixels were excluded from analysis (flagged as bad in GenePix). Additionally, failed probes, probes representing intergenic regions, probes representing rRNA, probes representing telomeres and probes representing the mitochondrial genome were excluded. For the remaining probes, the median of the ratios (total RNA; Rap1 depleted/non-depeleted cells) for each probe was converted to a log2 ratio. These total RNA log2 ratios (Rap1 depleted/non-depeleted cells) were then converted to z scores by centering at a mean of zero and scaling the standard deviation to one.

source_name: RT cDNA from Meiosis 9 hours; Rap1 depleted

label_protocol: Total RNA (30 micrograms) was reverse-transcribed using SuperScript II Reverse Transcriptase (Invitrogen) incorporating amino-allyl dUTP (Sigma) at a ratio of 3:2 with dTTP. Reactive Cy5 (Amersham) was coupled to the amino-allyl of the resulting DNA fragments in the presence of sodium bicarbonate.

growth_protocol: SHy20 (RAP1promoter::kanRtetO7- TATA/RAP1promoter::kanR-tetO7-TATA URA3::CMV-tetTA/URA3::CMV-tetTA) cells were grown overnight in YPD and then inoculated at an OD600 of 0.1 in YPA (containing 0.33 μg/ml doxycycline). Cells were grown in YPA for 8 hours at 30C and then the culture was split into a minus doxycycline (0.33 μg/ml; doxycycline) and a plus doxycycline sample (50 μg/ml doxycycline). The cells were returned to 30C and grown an additional 12 hours. Cells were harvested by centrifugation and washed with SM (either containing no doxycycline or 50 μg/ml doxycycline) resuspended in SM (either containing no doxycycline or 50 μg/ml doxycycline) at an OD600 of 2.0 in SM and incubated with vigorous shaking at 30C. Cells were collected from both minus and plus doxycycline samples after 20 hours in YPA media (25 ml of cells for ChIP and 15 ml for RNA isolation) and after 0, 3, 6, 9 or 12 hours in SM (11 ml for RNA isolation). Samples were pelleted and snap frozen in a dry ice/ethanol bath and stored at -80C until RNA abundance/expression analysis was performed.

extract_protocol: Total RNA was isolated from frozen samples using hot acid-phenol as previously described (Ausubel 1997).

value: Reverse transcribed total RNA

source_name: RT cDNA from Meiosis 9 hours

treatment_protocol: 0 ug/ml doxycycline


title: Rap1-depletion-Expression Meiosis TC - Meiosis 12hrs Replicate 2

description: Comparing RNA expression dynamics during meiosis timecourse in cells with wildtype Rap1 levels and cells depleted of Rap1. Meiosis (sporulation) 12 hour sample.

source_name: RT cDNA from Meiosis 12 hours

value: Meiosis 12 hours

source_name: RT cDNA from Meiosis 12 hours; Rap1 depleted


title: Rap1-depletion Rap1 ChIP - YPA 20hrs Replicate 3


title: Rap1-depletion-Expression Meiosis TC - Meiosis 12hrs Replicate 3


title: Rap1-depletion Rap1 ChIP - YPA 20hrs Replicate 1


title: Rap1-depletion Rap1 ChIP - YPA 20hrs Replicate 2


title: Rap1-depletion-Expression Meiosis TC - Meiosis 9hrs Replicate 3


title: Rap1-depletion-Expression Meiosis TC - Meiosis 9hrs Replicate 2


title: Rap1-depletion-Expression Meiosis TC - Meiosis 6hrs Replicate 5

description: Comparing RNA expression dynamics during meiosis timecourse in cells with wildtype Rap1 levels and cells depleted of Rap1. Meiosis (sporulation) 6 hour sample.

source_name: RT cDNA from Meiosis 6 hours; Rap1 depleted

value: Meiosis 6 hours

source_name: RT cDNA from Meiosis 6 hours


title: Rap1-depletion-Expression Meiosis TC - Meiosis 3hrs Replicate 5

description: Comparing RNA expression dynamics during meiosis timecourse in cells with wildtype Rap1 levels and cells depleted of Rap1. Meiosis (sporulation) 3 hour sample.

source_name: RT cDNA from Meiosis 3 hours; Rap1 depleted

source_name: RT cDNA from Meiosis 3 hours


title: Rap1-depletion-Expression Meiosis TC - Meiosis 0hrs Replicate 5

description: Comparing RNA expression dynamics during meiosis timecourse in cells with wildtype Rap1 levels and cells depleted of Rap1. Meiosis (sporulation) 0 hour sample.

source_name: RT cDNA from Meiosis 0 hours; Rap1 depleted

source_name: RT cDNA from Meiosis 0 hours


title: Rap1-depletion-Expression Meiosis TC - Meiosis 3hrs Replicate 3


title: Rap1-depletion-Expression Meiosis TC - Meiosis 0hrs Replicate 3


title: Rap1-depletion-Expression Meiosis TC - Meiosis 6hrs Replicate 2


title: Rap1-depletion-Expression Meiosis TC - Meiosis 0hrs Replicate 2


title: Rap1-depletion-Expression Meiosis TC - YPA 20hrs Replicate 5

description: Comparing RNA expression dynamics during meiosis timecourse in cells with wildtype Rap1 levels and cells depleted of Rap1. YPA (respiratory) growth sample.

source_name: RT cDNA from YPA 20 hours; Rap1 depleted

source_name: RT cDNA from YPA 20 hours


title: Rap1-depletion-Expression Meiosis TC - Meiosis 3hrs Replicate 2


title: Rap1-depletion-Expression Meiosis TC - YPA 20hrs Replicate 3


title: Rap1-depletion-Expression Meiosis TC - YPA 20hrs Replicate 2


title: Rap1 ChIP Meiosis TC - Meiosis 1.5hrs Replicate 3

source_name: Input DNA from Meiosis 1.5 hours

value: Input DNA

source_name: Rap1 ChIP DNA from Meiosis 1.5 hours


title: Expression Meiosis TC - Meiosis 12hrs Replicate 7

type: mixed

description: RNA expression dynamics during meiosis timecourse. Meiosis (sporulation) 12 hour sample.

hyb_protocol: Labeled reverse transcribed total RNA samples and genomic DNA references were competitively hybridized to yeast whole genome PCR based spotted arrays (resolution ~1kb). Hybridizations were carried out overnight at 65 C.

data_processing: Probes of poor quality by visual inspection, with more than 10% saturated pixels in either channel, with a background corrected sum of medians for both channels less than 500, or with fewer than 40 foreground pixels were excluded from analysis (flagged as bad in GenePix). Additionally, failed probes, probes representing intergenic regions, probes representing rRNA, probes representing telomeres and probes representing the mitochondrial genome were excluded. For the remaining probes, the median of the ratios (total RNA/Genomic DNA common reference) for each probe was converted to a log2 ratio. These log2 ratios (total RNA/Genomic DNA common reference) were then converted to z scores by centering at a mean of zero and scaling the standard deviation to one.

growth_protocol: Vegetative cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6-0.8 and 25 ml of cells were collected. Synchronous meiosis/sporulation was carried out by using YPD overnight cultures to inoculate YPA (1% yeast extract, 2% peptone, 2% potassium acetate) cultures at an OD600 of 0.1. YPA cultures were grown at 30C to an OD600 of 0.8-1.2 (about 16 hours). Cells were collected by centrifugation and washed with SM (2% potassium acetate). The cells were resuspended at an OD600 of 2.0 in SM (~600ml) and incubated in 2L flasks at 30C with shaking at 265 rpm. Cells were collected after 8 hours in YPA media (35 ml of cells) and after 0, 1.5, 3, 4.5, 6, 9 or 12 hours in SM (12.5 ml of cells). Samples were pelleted and snap frozen in a dry ice/ethanol bath and stored at -80C until RNA abundance/expression analysis was performed.

source_name: Genomic DNA common reference

label_protocol: Purified genomic DNA (4 micrograms) was labeled with Klenow (NEB) incorporating amino-allyl dUTP (Sigma) at a ratio of 3:2 with dTTP. Reactive Cy3 (Amersham) was coupled to the amino-allyl of the resulting DNA fragments in the presence of sodium bicarbonate.

extract_protocol: 100 ml of vegetative cells (OD600 0.6-0.8) were pelleted and resuspended in 2 ml lysis buffer (10 mM Tris-Cl pH 8.0, 100 mM NaCl, 1 mM EDTA, 1% SDS, 2% Triton X-100). The cells were split into 4 tubes (500 ul each) and an equal volume of phenol:chloroform:isoamyl-alcohol was added to each tube. The cells were then lysed with glass beads. The samples were spun down for 5 minutes at top speed and the aqueous layers was transfered to fresh tubes. Nucleic acids were precipitated with 1 ml of 95% ethanol and resuspended in 200 ul of 1X TE + 30 ug RNAse and incubated at 30 C for 30 minutes. 5 M NaCl was added to a final concentration of 500 mM and the samples were precipitated with isopropanol. Pellets were washed 2X with 70% ethanol and dried at room temperature for 30 minutes. The resulting genomic DNA was resuspended in 10 mM Tris-Cl pH 7.4 and pooled and the concentration was determined with a spectrophotometer.

value: Genomic DNA common reference


title: Expression Meiosis TC - Meiosis 12hrs Replicate 1


title: Expression Meiosis TC - Meiosis 12hrs Replicate 2


title: Expression Meiosis TC - Meiosis 12hrs Replicate 6


title: Expression Meiosis TC - Meiosis 12hrs Replicate 4


title: Expression Meiosis TC - Meiosis 12hrs Replicate 5


title: Rap1-depletion-Expression Meiosis TC - Meiosis 12hrs Replicate 5


title: Expression Meiosis TC - Meiosis 9hrs Replicate 7

description: RNA expression dynamics during meiosis timecourse. Meiosis (sporulation) 9 hour sample.

value: Meiosis 9 hours


title: Rap1-depletion-Expression Meiosis TC - Meiosis 6hrs Replicate 3


title: Expression Meiosis TC - Meiosis 12hrs Replicate 3


title: Expression Meiosis TC - Meiosis 9hrs Replicate 2


title: Expression Meiosis TC - Meiosis 9hrs Replicate 4


title: Expression Meiosis TC - Meiosis 9hrs Replicate 5


title: Expression Meiosis TC - Meiosis 9hrs Replicate 6


title: Expression Meiosis TC - Meiosis 6hrs Replicate 7

description: RNA expression dynamics during meiosis timecourse. Meiosis (sporulation) 6 hour sample.


title: Expression Meiosis TC - Meiosis 6hrs Replicate 4


title: Expression Meiosis TC - Meiosis 9hrs Replicate 1


title: Expression Meiosis TC - Meiosis 6hrs Replicate 5


title: Expression Meiosis TC - Meiosis 6hrs Replicate 3


title: Expression Meiosis TC - Meiosis 6hrs Replicate 2


title: Expression Meiosis TC - Meiosis 4.5hrs Replicate 6

description: RNA expression dynamics during meiosis timecourse. Meiosis (sporulation) 4.5 hour sample.

source_name: RT cDNA from Meiosis 4.5 hours


title: Expression Meiosis TC - Meiosis 4.5hrs Replicate 7


title: Expression Meiosis TC - Meiosis 4.5hrs Replicate 2


title: Expression Meiosis TC - Meiosis 6hrs Replicate 6


title: Expression Meiosis TC - Meiosis 4.5hrs Replicate 1


title: Expression Meiosis TC - Meiosis 6hrs Replicate 1


title: Expression Meiosis TC - Meiosis 4.5hrs Replicate 3


title: Expression Meiosis TC - Meiosis 4.5hrs Replicate 4


title: Expression Meiosis TC - Meiosis 9hrs Replicate 3


title: Expression Meiosis TC - Meiosis 4.5hrs Replicate 5


title: Expression Meiosis TC - Meiosis 3hrs Replicate 7

description: RNA expression dynamics during meiosis timecourse. Meiosis (sporulation) 3 hour sample.

value: Meiosis 3 hours


title: Expression Meiosis TC - Meiosis 3hrs Replicate 6


title: Expression Meiosis TC - Meiosis 3hrs Replicate 4


title: Expression Meiosis TC - Meiosis 3hrs Replicate 2


title: Expression Meiosis TC - Meiosis 3hrs Replicate 3


title: Expression Meiosis TC - Meiosis 3hrs Replicate 1


title: Expression Meiosis TC - Meiosis 3hrs Replicate 5


title: Expression Meiosis TC - Meiosis 1.5hrs Replicate 7

description: RNA expression dynamics during meiosis timecourse. Meiosis (sporulation) 1.5 hour sample.

source_name: RT cDNA from Meiosis 1.5 hours

value: Meiosis 1.5 hours


title: Expression Meiosis TC - Meiosis 1.5hrs Replicate 5


title: Expression Meiosis TC - Meiosis 1.5hrs Replicate 6


title: Expression Meiosis TC - Meiosis 1.5hrs Replicate 4


title: Expression Meiosis TC - Meiosis 1.5hrs Replicate 3


title: Expression Meiosis TC - Meiosis 1.5hrs Replicate 2


title: Rap1 ChIP Meiosis TC - Meiosis 4.5hrs Replicate 2

description: Rap1 binding dynamics during meiosis timecourse. Rap1 ChIP meiosis (sporulation) 4.5 hour sample.

source_name: Rap1 ChIP DNA from Meiosis 4.5 hours

value: Meiosis 4.5 hours

source_name: Input DNA from Meiosis 4.5 hours


title: Expression Meiosis TC - Meiosis 0hrs Replicate 6

description: RNA expression dynamics during meiosis timecourse. Meiosis (sporulation) 0 hour sample.

value: Meiosis 0 hours


title: Expression Meiosis TC - Meiosis 0hrs Replicate 5


title: Expression Meiosis TC - Meiosis 1.5hrs Replicate 1


title: Expression Meiosis TC - Meiosis 0hrs Replicate 7


title: Expression Meiosis TC - YPA 8hrs Replicate 3

description: RNA expression dynamics during meiosis timecourse. YPA (respiratory) growth sample.

source_name: RT cDNA from YPA 8 hours

value: YPA 8 hours


title: Expression Meiosis TC - YPA 8hrs Replicate 4


title: Expression Meiosis TC - YPA 8hrs Replicate 5


title: Expression Meiosis TC - YPA 8hrs Replicate 2


title: Expression Meiosis TC - Meiosis 0hrs Replicate 4


title: Expression Meiosis TC - Meiosis 0hrs Replicate 1


title: Expression Meiosis TC - Meiosis 0hrs Replicate 2


title: Expression Meiosis TC - YPD Replicate 7

description: RNA expression dynamics during meiosis timecourse. YPD (logarithmic) growth sample.

source_name: RT cDNA from YPD

value: YPD


title: Expression Meiosis TC - YPA 8hrs Replicate 7


title: Expression Meiosis TC - YPA 8hrs Replicate 1


title: Expression Meiosis TC - Meiosis 0hrs Replicate 3


title: Expression Meiosis TC - YPD Replicate 6


title: Expression Meiosis TC - YPD Replicate 5


title: Expression Meiosis TC - YPD Replicate 1


title: Expression Meiosis TC - YPD Replicate 2


title: Expression Meiosis TC - YPD Replicate 4


title: Expression Meiosis TC - YPA 8hrs Replicate 6


title: Expression Meiosis TC - YPD Replicate 3


title: Slide 53_Anaerobic culture_CO gas_biol rep 3_Cy3 40 Cy5 0

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-4

hyb_protocol: For hybridization to the microarray slides, 400 ng cDNA was added to 25 μl 2 x Hi-RMP Hybridization Buffer and 5 μl 10 x Gene Expression Blocking Agent (Agilent Technologies) to give 50 μl total volume. Custom Gene Expression Microarray slides each containing 8 x 15K arrays were purchased from Agilent Technologies. For hybridization one 8 x Gasket Slide was placed inside a Microarray Hybridization Chamber and samples loaded for 8 different conditions, followed by placement of the microarray slide over the gasket. After sealing the chamber the arrays were incubated at 65 °C, rotating at 10 rpm for ~17 h. Following incubation, the slides were washed in Gene Expression Wash Buffer 1 for 1 min, followed by washing in Gene Expression Wash Buffer 2 for 1 min. Slides were dried and scanned in a microarray scanner (Agilent).

scan_protocol: Scanned on an Agilent DNA microarray scanner with SureScan high-resolution technology

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization.

organism: Escherichia coli

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L/min for 40min

label_protocol: cDNA synthesis was carried out using 16 μg of RNA, primed with 5 μg Random Primers (Invitrogen). Reaction mixes (30 μl) containing 0.5 mM dATP, dTTP, and dGTP, 0.2 mM dCTP, and 67 μM Cy-3 or Cy-5-dCTP were incubated at 25 °C for 5 min, then at 50 °C overnight with 300 U of Superscript III Reverse Transcriptase (Invitrogen). Following synthesis, cDNA was purified using a PCR purification kit (Qiagen).

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

tag: treatment

tag: time

value: Wild type strain MG1655

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 5min


title: Slide 53_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 2.5

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-6

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L/min for 2.5min

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 20min


title: Slide 53_Anaerobic culture_CO gas_biol rep 3_Cy3 80 Cy5 0

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-3

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L/min for 80min

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 2.5min


title: Slide 53_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 5

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-5

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L/min for 5min

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 10min


title: Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 10 2

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-10

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L/min for 10min

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 80min


title: Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 20

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L/min for 20min

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 5min


title: Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 5

value: Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L/min

value: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3


title: Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 10

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 2.5min


title: Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 2.5

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 40min


title: Slide 39_Anaerobic culture_CO gas_biol rep 2_Cy3 80 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 20min


title: Slide 39_Anaerobic culture_CO gas_biol rep 2_Cy3 40 Cy5 0

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-9

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 10min


title: Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 5 Cy5 0


title: Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 5 Cy5 0


title: Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 2.5 Cy5 0


title: Slide 39_Anaerobic culture_CO gas_biol rep 1_Cy3 80 Cy5 0


title: Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 80

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-8


title: Slide 39_Anaerobic culture_CO gas_biol rep 1_Cy3 40 Cy5 0


title: Slide 39_Anaerobic culture_CO gas_biol rep 1_Cy3 20 Cy5 0


title: Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 80 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 0.1L/min CO gas for 80min

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 80min


title: Slide 39_Anaerobic culture_CO gas_biol rep 1_Cy3 10 Cy5 0


title: Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 5


title: Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 40

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-7

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L/min for 40min


title: Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 2.5 Cy5 0

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L/min for 2.5min


title: Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 10


title: Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 20


title: Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 40 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 0.1L/min CO gas for 40min

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 40min


title: Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 2.5


title: Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 40


title: Slide 39_Anaerobic culture_CO gas_biol rep 2_Cy3 10 Cy5 0


title: Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 10 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 0.1L/min CO gas for 10min

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 10min


title: Slide 39_Anaerobic culture_CO gas_biol rep 2_Cy3 20 Cy5 0


title: Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 20 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 0.1L/min CO gas for 20min

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 20min


title: Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 2.5 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 0.1L/min CO gas for 2.5min

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 2.5min


title: Slide 31_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 20

value: Continuous aerobically grown cultures in Evans medium, exposed to 0.1L/min CO gas

value: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3


title: Slide 31_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 10


title: Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 5 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 0.1L/min CO gas for 5min

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 5min


title: Slide 31_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 5


title: Slide 31_Aerobic culture_CO gas_biol rep 1_Cy3 20 Cy5 0


title: Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 40


title: tumor metformin 4

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: tumor, 2mg metformin

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Tumor (mouse): Each mouse was inoculated with HuCCT-1 cells (5×106cells/animal) subcutaneously on the flank regions of the mouse.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: Tumor: The metformin-treated group was injected 5 times a week intraperitoneally (i.p.) at 2 mg/body per day for 31 days.

value: tumor

tag: disease type

value: cholangiocarcinoma


title: Slide 31_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 2.5


title: Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 80


title: Slide 31_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 80


title: Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 40


title: Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 80 Cy5 0


title: tumor metformin 2


title: tumor metformin 3


title: Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 2.5


title: Slide 31_Aerobic culture_CO gas_biol rep 1_Cy3 10 Cy5 0


title: Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 5


title: tumor control 3

source_name: tumor control, 0mg


title: tumor metformin 1


title: Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 20


title: Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 5 Cy5 0


title: tumor control 2


title: tumor control 1


title: tumor control 4


title: Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 10

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 0.1L/min CO gas for 10 min

value: 10 min


title: Slide 31_Aerobic culture_CO gas_biol rep 1_Cy3 40 Cy5 0


title: Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 2.5 Cy5 0


title: HS [6029437028_F]

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol with HiScanSQ.

data_processing: The data were quantile normalised using GenomeStudio (Illumina).

source_name: urinary extracellular vesicles, healthy

label_protocol: cRNA were prepared with the Illumina DASL kit for Illumina arrays.

extract_protocol: RNA was extracted using the miRCURY RNA isolation kit (Exiqon, according to the manufacturer's protocol, DNase I - Qiagen - digestion) and eluted in 50 μL of elution buffer. Then, an aliquot was run on an RNA Pico 6000 chip (Agilent, CA) using an Agilent Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA) to assess quantity and integrity.

tag: tissue

value: urinary extracellular vesicles

tag: disease status

value: healthy

tag: gender

value: M


title: HS [6029437028_E]


title: RCC [6029437028_K]

source_name: urinary extracellular vesicles, ccRCC

value: clear-cell renal cell carcinoma (ccRCC)


title: RCC [6029437028_H]


title: HS [6029437028_D]


title: HS [6029437028_C]


title: HS [6029437028_B]

value: F


title: RCC [5993419030_G]


title: HS [5993419025_K]


title: RCC [5993419025_E]


title: HS [5993419025_I]


title: HS [6029437028_G]


title: HS [5993419025_H]


title: HS [6029437028_A]


title: hNHeps miRNA

city: Yonago

first: Tomohiko

last: Sakabe

state: Tottori

address: Nishi-cho 86

institute: Tottori University

description: SH39R13.xls (Data4)

hyb_protocol: Fragmented RNA was hybridized on the Oligo chip for 16 hour at 37˚C.

scan_protocol: Human Oligo chip was scanned by a ProScanArray scanner.

data_processing: To generate the normalized data, the raw signal intensity were subtracted with the Background mean and normalized to the value in which the median intensity was 25.

source_name: Normal

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (thermo fisher scientific). CyeDye coupling was performed according to the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA was extracted with TRIzol Reagent

value: human normal hepatocytes


title: RCC [5993419025_D]


title: CD44+ HuH7 miRNA

description: SH39R13.xls (Data3)

source_name: CSC

value: CD44+ HuH7


title: RCC [5993419025_G]


title: RCC [5993419025_B]


title: CD44- HuH7 miRNA

description: SH39R13.xls (Data2)

source_name: non-CSC

value: CD44- HuH7


title: RCC [5993419030_I]


title: RCC [5993419025_F]


title: FAIRE Meiosis TC - Meiosis 3hrs Replicate 4

description: FAIRE open chromatin dynamics during meiosis timecourse. Meiosis (sporulation) 3 hour sample.

hyb_protocol: Four micrograms of fluorescently labeled reference DNA and four micrograms of fluorescently labeled FAIRE DNA were used in the hybridization. Samples were competitively hybridized with the reference at 52C for 16 hours in a Maui hybridization chamber to yeast whole genome 4 x 44k tiling microarrays (Agilent; ~270 bp resolution).

data_processing: Probes of poor quality by visual inspection, with more than 10% saturated pixels in either channel, or with a background corrected sum of medians for both channels less than 500, were excluded from analysis (flagged as bad in GenePix). Additionally, those probes representing the mitochondrial genome were excluded. For the remaining probes, the median of the ratios (FAIRE/reference) for each probe was converted to a log2 ratio. These log2 ratios (FAIRE/reference) were then converted to z scores by centering at a mean of zero and scaling the standard deviation to one.

source_name: FAIRE enriched DNA from Meiosis 3 hours

label_protocol: ~100 ng starting material was amplified using the Whole-Genome Amplification kit (Sigma) as described (O'Geen, Nicolet, Blahnik, Green and Farnham 2006). Two micrograms of amplified DNA was labeled with Cy5 conjugated dUTP using the BioPrime Array CGH kit (Invitrogen). DNA concentration and dye incorporation were measured using a Nanodrop spectrometer.

growth_protocol: Vegetative cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6-0.8 and 100 ml of cells were collected. Synchronous meiosis/sporulation was carried out by using YPD overnight cultures to inoculate YPA (1% yeast extract, 2% peptone, 2% potassium acetate) cultures at an OD600 of 0.1. YPA cultures were grown at 30C to an OD600 of 0.8-1.2 (about 16 hours). Cells were collected by centrifugation and washed with SM (2% potassium acetate). The cells were resuspended at an OD600 of 2.0 in SM (~600ml) and incubated in 2L flasks at 30C with shaking at 265 rpm. Cells were collected after 0, 1.5, or 3 hours in SM (50 ml of cells). All samples were fixed with 1% formaldehyde for 20 minutes at room temperature and washed twice with 1X cold PBS. Samples were then snap frozen in a dry ice/ethanol bath and stored at -80C until FAIRE enrichment was performed.

extract_protocol: 50 ml of cells were fixed with 1% formaldehyde for 20 minutes at room temperature and washed twice with 1X cold PBS. The samples were then snap frozen in a dry ice/ethanol bath and stored at -80C. FAIRE was carried out as described (Hogan, Lee and Lieb 2006). Briefly, cells were thawed and lysed with glass beads and the chromatin was sheared to an average size of ~800 bp by sonication as measured by agarose gel electrophoresis. 1 mg of extract from crosslinked FAIRE samples was phenol-chloroform extracted to remove proteins and protein-associated DNA. The resulting DNA samples were further purified using Zymo Clean and Concentrator kit and the concentration was determined with a spectrophotometer.

tag: strain

value: SK1 yeast strain SHy002

value: Meiosis 3 hours

value: FAIRE enriched DNA

source_name: Genomic DNA common reference

extract_protocol: 100 ml of UNFIXED vegetative cells (OD600 0.6-0.8) were washed twice with 1X cold PBS. The cells were resuspended in lysis buffer and lysed with glass beads. The chromatin was sheared to an average size of ~800 bp by sonication as measured by agarose gel electrophoresis. The UNFIXED reference samples were phenol-chloroform extracted to remove proteins. The resulting sonicated genomic DNA was precipitated with isopropanol and resuspended in 10 mM Tris-Cl pH 7.4 and the concentration was determined with a spectrophotometer.

value: Genomic DNA common reference


title: FAIRE Meiosis TC - Meiosis 3hrs Replicate 6


title: FAIRE Meiosis TC - Meiosis 3hrs Replicate 1


title: FAIRE Meiosis TC - Meiosis 1.5hrs Replicate 6

description: FAIRE open chromatin dynamics during meiosis timecourse. Meiosis (sporulation) 1.5 hour sample.

value: Meiosis 1.5 hours

source_name: FAIRE enriched DNA from Meiosis 1.5 hours


title: RCC [5993419025_A]

tag: age


title: HS [5993419025_J]


title: FAIRE Meiosis TC - Meiosis 1.5hrs Replicate 4


title: RCC [5993419025_C]


title: RCC [6029437028_I]


title: FAIRE Meiosis TC - Meiosis 0hrs Replicate 6

description: FAIRE open chromatin dynamics during meiosis timecourse. Meiosis (sporulation) 0 hour sample.

value: Meiosis 0 hours

source_name: FAIRE enriched DNA from Meiosis 0 hours


title: FAIRE Meiosis TC - Meiosis 0hrs Replicate 4


title: FAIRE Meiosis TC - Meiosis 1.5hrs Replicate 1


title: FAIRE Meiosis TC - Meiosis 0hrs Replicate 1


title: FAIRE Meiosis TC - YPD Replicate 1

description: FAIRE open chromatin dynamics during meiosis timecourse. YPD (logarithmic) growth sample.

value: YPD

source_name: FAIRE enriched DNA from YPD


title: FAIRE Meiosis TC - YPD Replicate 4

extract_protocol: 100 ml of cells were fixed with 1% formaldehyde for 20 minutes at room temperature and washed twice with 1X cold PBS. The samples were then snap frozen in a dry ice/ethanol bath and stored at -80C. FAIRE was carried out as described (Hogan, Lee and Lieb 2006). Briefly, cells were thawed and lysed with glass beads and the chromatin was sheared to an average size of ~800 bp by sonication as measured by agarose gel electrophoresis. 1 mg of extract from crosslinked FAIRE samples was phenol-chloroform extracted to remove proteins and protein-associated DNA. The resulting DNA samples were further purified using Zymo Clean and Concentrator kit and the concentration was determined with a spectrophotometer.


title: Astrocyte_non IgG_LPS(-)_rep1

city: Izumo

first: Kunihiro

last: Ichinose

address: 89-1 Enya-cho

department: Department of Rheumatology

institute: Shimane University Faculty of Medicine

hyb_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

scan_protocol: We followed manufacturer's protocol, and used GenePix 4400A. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

data_processing: CodeLink Expression Analysis v5.0 software, Quantile normalization

source_name: Human astrocyte exposure to non IgG for 24 h

growth_protocol: Normal human astrocytes (NHAs) isolated from human fetal brains (Clonetics normal human astrocytes; Lonza, Switzerland) were maintained in RPMI 1640 supplemented with 10 % fetal calf serum and seeded into 6-well tissue culture plates to a density of 4 × 10^5 cells 24 hours prior to experimentation.

extract_protocol: RNeasy mini kit (Qiagen, Miami, FL) was used.

value: astrocytes

value: non IgG for 24 h


title: Astrocyte_norm IgG_LPS(+)_rep4

source_name: Human astrocyte exposure to normal IgG with LPS (1μg/ml) for 24 h

label_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

value: normal IgG with LPS (1μg/ml) for 24 h


title: Astrocyte_SBSN IgG_LPS(-)_rep5

source_name: Human astrocyte exposure to SBSN IgG for 24 h

value: SBSN IgG for 24 h