title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 3 days - rep2

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 3 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 3 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 3 days - rep3

status: Public on Jan 13 2016

type: RNA

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

label: biotin

molecule: total RNA

organism: Vitis riparia

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines. Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude with 15h day using supplemental lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

extract_protocol: Modified Pine Buffer RNA Extraction Procedure

tag: germplasm name

value: Vitis riparia PI588259

tag: organism part

value: second order axillary bud

tag: cell type

tag: development stage

value: paradormancy

tag: age

value: 31 days after bud break

tag: growth media

value: peat/perlite/soil


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 3 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 14 days - rep3

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 14 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 14 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 14 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 1 days - rep3

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 1 day of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 1 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 1 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 28 days - rep1

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 28 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 28 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 3 days - rep2

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 3 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 3 days - rep3


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 42 days - rep3

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 42 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 42 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 28 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 1 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 42 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 7 days - rep3

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 7 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 7 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 28 days - rep3


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 42 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 3 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 14 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 14 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 21 days - rep3

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 21 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 21 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 21 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 14 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 21 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 1 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 1 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 14 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 7 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 42 days - rep1

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 42 days)


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 42 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 28 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 28 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 1 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 42 days - rep3


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 28 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 21 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 21 days)


title: treated shoot 2

city: Honolulu

first: Kazue

last: Ishihara

state: HI

address: 1955 East-West Rd AgSci 218

department: Molecular Biosciences and Bioengineering

institute: University of Hawaii at Manoa

hyb_protocol: Hybridization was performed by Carver Center for Genomics, University of Iowa, IA, USA following Agilent standard operating protocol.

scan_protocol: Scanning was performed by Carver Center for Genomics, University of Iowa, IA, USA following Agilent standard operating protocol.

data_processing:
All the data extraction was done using the default setting for one-color gene expression arrays (protocol GE1_1105_Oct12) using the Feature Extraction v.11.5.1.1 software
[final, processed data] average intensity for target

organism: Leucaena leucocephala

source_name: Shoot tissue, treated with PEG6003

label_protocol: Labelling was performed by Carver Center for Genomics, University of Iowa, IA, USA following Agilent standard operating protocol.

growth_protocol: Leucaena leucocephala seedlings were grown in pots containing a vermiculite-perlite mixture for four weeks at 25 °C +/- 2° C with a 16/8-h light/dark photoperiod with an irradiance of 30 µmol s-1 m-1.  Hoagland's solution was used to water the seedlings.

extract_protocol: Qiagen Rneasy Plant Kit and Takara Fruit-mate were used to extract total RNA from the tissues of L. leucocephala.

treatment_protocol: Fifteen % PEG6000 in Hoagland's solution was used as a drought treatment.  After 48 hours, shoots and roots of the seedlings were collected and immediately frozen in liquid nitrogen.  Untreated seedlings, collected at the same time, were used as control.

tag: developmental stage

value: seedling

tag: tissue

value: shoot

tag: treatment

value: seedlings watered with 15% PEG6000 in Hoagland's solution

tag: stress

value: drought


title: treated shoot 1

source_name: Shoot tissue, treated with PEG6002


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 28 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 1 days - rep2


title: treated root 1

source_name: Root tissue, treated with PEG6000


title: control shoot 2

source_name: Shoot tissue, untreated with PEG6001

value: root

value: seedlings watered with Hoagland's solution

value: control


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 21 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 14 days - rep2

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 14 days)


title: control shoot 1

source_name: Shoot tissue, untreated with PEG6000


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 7 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 21 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 1 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 1 days)


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 14 days - rep3


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 3 days - rep1

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 3 days)


title: treated root 2

source_name: Root tissue, treated with PEG6001


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 3 days - rep3


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 7 days - rep2

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 7 days)


title: control root 2

source_name: Root tissue, untreated with PEG6001


title: control root 1

source_name: Root tissue, untreated with PEG6000


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 7 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 7 days - rep3


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 1 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 3 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 42 days - rep1

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 42 days)


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 42 days - rep2


title: GC7-MMC-3

type: genomic

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: Genomic DNA extracted from stem cells or blood samples were genotyped using HumanOmniZhongHua-8 v1.1 Beadchip Kit (Illumina).

hyb_protocol: Followed Illumina standard protocol

scan_protocol: Followed Illumina standard protocol

data_processing: GenomeStudio Software (Illumina)

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Patient 12_GCSC_rep 2

label_protocol: Followed Illumina standard protocol

growth_protocol: Human gastric cardia and Barrett's esopahus stem cells from endoscopic biopsy were cultured on 3T3 feeder layer.

extract_protocol: Genomic DNA from cells were extracted using DNeasy blood and tissue kit (Qiagen)

treatment_protocol: Two independent pedigrees were isolated and collected, and patient-matched blood are used as control

tag: patient

value: Patient 12

value: GCSC


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 42 days - rep3


title: BE7-MMC2

source_name: Patient 12_BESC_rep 1

value: BESC


title: BE blood 7

source_name: Patient 12_Blood

value: Blood


title: GC38-2

source_name: Patient 10_GCSC_rep 2

value: Patient 10


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 1 days - rep2

value: Vitis riparia PI588259


title: GC38-1

source_name: Patient 10_GCSC_rep 1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 21 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 21 days)

value: second order axillary bud


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 14 days - rep1

value: paradormancy


title: BE7-MMC3

source_name: Patient 12_BESC_rep 2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 14 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 14 days)

value: 31 days after bud break


title: BE38-4

source_name: Patient 10_BESC_rep 2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 21 days - rep2

value: peat/perlite/soil


title: GC7-MMC-2

source_name: Patient 12_GCSC_rep 1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 28 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 28 days)


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 28 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 21 days - rep1


title: BE38-3

source_name: Patient 10_BESC_rep 1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 7 days - rep2

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 7 days)


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 7 days - rep3


title: BE19 CRD4

source_name: Patient 9_GCSC_rep 2

value: Patient 9


title: BE19 BE4

source_name: Patient 9_BESC_rep 2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 14 days - rep1


title: BE19 BLD

source_name: Patient 9_Blood


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 3 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 3 days)


title: Patient 38 blood

source_name: Patient 10_Blood


title: BE19 CRD1

source_name: Patient 9_GCSC_rep 1


title: 9C1

source_name: Patient 8_GCSC_rep 1

value: Patient 8


title: BE19 BE3

source_name: Patient 9_BESC_rep 1


title: 9BE1

source_name: Patient 8_BESC_rep 1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 1 days - rep1

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 1 days)

value: V. riparia (VR, PI588259)


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 1 days - rep3


title: GC20-MMC-14

source_name: Patient 7_GCSC_rep 2

value: Patient 7


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 3 days - rep1


title: 9C2

source_name: Patient 8_GCSC_rep 2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 1 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 3 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 7 days - rep1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 42 days - rep3

organism: Vitis hybrid cultivar

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 42 days)

value: Seyval (SV, Seyve Villard 5-276)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 28 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 28 days)


title: 9BE4

source_name: Patient 8_BESC_rep 2


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 21 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 21 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 42 days - rep1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 21 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 14 days - rep2

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 14 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 21 days - rep3


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 28 days - rep1


title: GC20-MMC-2

source_name: Patient 7_GCSC_rep 1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 14 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 14 days)


title: genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 28 days - rep1

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 28 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 28 days - rep2


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 14 days - rep3


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 42 days - rep2


title: BE20-MMC-pooled

source_name: Patient 7_BESC (pool)_ pool

value: BESC (pool)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 7 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 7 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 14 days - rep1


title: GC10-2 B

source_name: Patient 6_GCSC_rep 2

value: Patient 6


title: BE20-MMC-4

source_name: Patient 7_BESC_rep 2


title: BE10-2

source_name: Patient 6_BESC_rep 2


title: 9BE(blood)

source_name: Patient 8_Blood


title: BE20-MMC-3

source_name: Patient 7_BESC_rep 1


title: GC23-3

source_name: Patient 5_GCSC_rep 2

value: Patient 5


title: BE blood 20

source_name: Patient 7_Blood


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 3 days - rep1

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 3 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 7 days - rep2


title: BE10-8

source_name: Patient 6_BESC_rep 1


title: BE blood 10

source_name: Patient 6_Blood


title: 20C2

source_name: Patient 4_GCSC_rep 1

value: Patient 4

value: GCSC


title: 20C3

source_name: Patient 4_GCSC_rep 2


title: BE23-10

source_name: Patient 5_BESC_rep 2

value: BESC


title: GC23-2

source_name: Patient 5_GCSC_rep 1


title: GC10-1 B

source_name: Patient 6_GCSC_rep 1


title: 20BE1

source_name: Patient 4_BESC_rep 1


title: BE23-6

source_name: Patient 5_BESC_rep 1


title: Blood 23_BE

source_name: Patient 5_Blood

value: Blood


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 42 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 42 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 3 days - rep2


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 1 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 1 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 28 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 28 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 7 days - rep1

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 7 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 42 days - rep1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 28 days - rep1


title: BE8 CRD2

source_name: Patient 3_GCSC_rep 2

value: Patient 3


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 1 days - rep2

value: second order axillary bud


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 1 days - rep1

value: paradormancy


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 28 days - rep2

value: 31 days after bud break


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 3 days - rep3

value: peat/perlite/soil


title: 20(blood)

source_name: Patient 4_Blood


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 42 days - rep2


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 21 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 21 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 21 days - rep2


title: BE8 BE10

source_name: Patient 3_BESC_rep 2


title: BE8 CRD1

source_name: Patient 3_GCSC_rep 1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 14 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 14 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 14 days - rep1


title: GC5-2-4

source_name: Patient 2_GCSC_rep 2

value: Patient 2


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 7 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 7 days)


title: BE5 (11-1)

source_name: Patient 2_BESC_rep 2


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 21 days - rep1


title: BE8 BE4

source_name: Patient 3_BESC_rep 1


title: BE8 BLD

source_name: Patient 3_Blood


title: 20BE2

source_name: Patient 4_BESC_rep 2


title: Blood patient 5#

source_name: Patient 2_Blood


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 14 days - rep2


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 3 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 3 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 7 days - rep1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 7 days - rep2


title: GC5-1-3

source_name: Patient 2_GCSC_rep 1


title: BE5 (10-1)

source_name: Patient 2_BESC_rep 1


title: plasma_MDS_12

city: Prague 2

first: Michaela

last: Dostalova Merkerova

address: U nemocnice 1

department: Department of Genomics

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by incubation at 100°C for 5 min. Finally, denatured labeled probes were pipetted onto assembled Agilent miRNA Microarray and hybridized for 20 hours at 5°C with 20 RPM rotating in Agilent Hybridization oven.

scan_protocol: The hybridized images were scanned using Agilent DNA microarray scanner and quantified with Agilent Feature Extraction Software.

data_processing: Quality control and background subtraction of raw microarray data were carried out by Agilent Feature Extraction Software. Only those miRNAs whose signal was detected in more than 4 samples at least in one analyzed group were included for further analysis. Quantile normalization was performed in R statistical environment (www.r-project.org).

source_name: peripheral blood plasma RNA, MDS patient no. 12

label_protocol: Labeling was performed using Agilent miRNA Labeling and Hybridization kit according to the manufacturer's instructions. Total RNA (350 ng) was dephosphorylated with calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with DMSO and 10 min incubation at 100°C. Dephosphorylated RNA was ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

growth_protocol: Czech patients with primary MDS and healthy donors with no known history of previous malignancy, chemotherapy or radiation therapy were tested.

extract_protocol: Plasma was separated from peripheral blood (centrifugation at 460 g, 4°C for 10 minutes) and stored at -80°C. After thawing on ice, plasma samples were centrifuged (12000 g, 4°C for 10 minutes) to dispose of cell debris. Samples (500 μl) were further homogenized with equal volume of Trizol LS reagent (Invitrogen, Basel, Switzerland), incubated at room temperature (5 minutes) and centrifuged (12000 g, 4°C for 10 minutes). Aqueous phase containing RNA was transferred to a fresh tube. To maximize RNA recovery, we reextracted the organic phase again. RNA was precipitated by 100% isopropanol (500 μl) with 100 μg of glycogen, incubated for 10 minutes at room temperature and  subsequently centrifuged (12000 g, 4°C for 10 minutes). The pellet was washed with 75% ethanol, spinned at 7500 g, 4°C for 5 minutes and air dried. RNA was dissolved in RNase-free water and stored at -80°C.

treatment_protocol: The patients has not been subjected to the disease therapy or hematopoietic stem cell transplantation before the blood collection.

tag: gender

value: female

tag: diagnosis

tag: iPSs risk category

tag: sample type

value: blood plasma


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 1 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 1 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 3 days - rep1


title: plasma_MDS_13

source_name: peripheral blood plasma RNA, MDS patient no. 13

value: male


title: plasma_MDS_9

source_name: peripheral blood plasma RNA, MDS patient no. 9


title: plasma_MDS_11

source_name: peripheral blood plasma RNA, MDS patient no. 11


title: plasma_MDS_8

source_name: peripheral blood plasma RNA, MDS patient no. 8


title: 1BE

source_name: Patient 1_BESC_rep 2

value: Patient 1


title: 1C10.3

source_name: Patient 1_GCSC_rep 2


title: 7C2

description: Genomic DNA extracted from stem cells or blood samples were genotyped using HumanOmniZhongHua-8 v1.0 Beadchip Kit (Illumina).

source_name: Patient 11_GCSC_rep 2

value: Patient 11


title: plasma_MDS_10

source_name: peripheral blood plasma RNA, MDS patient no. 10

value: high


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 3 days - rep2

value: Seyval (SV, Seyve Villard 5-276)


title: plasma_MDS_14

source_name: peripheral blood plasma RNA, MDS patient no. 14


title: plasma_MDS_7

source_name: peripheral blood plasma RNA, MDS patient no. 7

value: RARS


title: plasma_MDS_4

source_name: peripheral blood plasma RNA, MDS patient no. 4

value: RCMD


title: plasma_MDS_3

source_name: peripheral blood plasma RNA, MDS patient no. 3


title: plasma_MDS_2

source_name: peripheral blood plasma RNA, MDS patient no. 2

value: low


title: 7DE2

source_name: Patient 11_BESC_rep 2

value: BESC


title: plasma_MDS_6

source_name: peripheral blood plasma RNA, MDS patient no. 6


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 1 days - rep1


title: plasma_MDS_5

source_name: peripheral blood plasma RNA, MDS patient no. 5


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 42 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 42 days)


title: Patient 7 blood

source_name: Patient 11_Blood

value: Blood


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 42 days - rep3

value: second order axillary bud


title: 7C1

source_name: Patient 11_GCSC_rep 1

value: GCSC


title: plasma_control_6

source_name: peripheral blood plasma RNA, healthy donor no. 6

value: healthy


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 42 days - rep1

value: paradormancy

value: 31 days after bud break

value: peat/perlite/soil


title: plasma_MDS_1

source_name: peripheral blood plasma RNA, MDS patient no. 1

value: female

value: blood plasma


title: 1DE1

source_name: Patient 1_BESC_rep 1

value: Patient 1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 28 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 28 days)


title: plasma_control_5

source_name: peripheral blood plasma RNA, healthy donor no. 5


title: plasma_control_2

source_name: peripheral blood plasma RNA, healthy donor no. 2

value: male


title: plasma_control_1

source_name: peripheral blood plasma RNA, healthy donor no. 1


title: Patient 1 blood

source_name: Patient 1_Blood


title: 1C1

source_name: Patient 1_GCSC_rep 1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 28 days - rep1


title: 7DE1

source_name: Patient 11_BESC_rep 1

value: Patient 11


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 21 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 21 days)

value: Seyval (SV, Seyve Villard 5-276)


title: 79A infected.  100 DPI. Rep 2 (failed QC)

city: Easter Bush Campus

first: James

last: Vincenti

state: Midlothian

address: The Roslin Institute

department: Neurobiology Division

country: United Kingdom

institute: The Roslin Institute, The University of Edinburgh

description: Failed QC and not anaysed any futher in our study.  Suspect this was due to lowest RNA volume.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix Expression Console

organism: Mus musculus

source_name: Total RNA extracted from whole mouse brain microglia isolated immediately after cull.  Taken at 100 dpi following infection with 0.02 ml of 0.02 w/v 79A strain prion disease (injected i.p.).

label_protocol: NuGen Encore® Biotin module biotin labelling process

extract_protocol: none provided by the submitter

tag: strain

value: BALB/cJ-Fms-EGFP/-

value: Brain

tag: rna volume (ng/µl)


title: plasma_control_4

source_name: peripheral blood plasma RNA, healthy donor no. 4


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 28 days - rep2

tag: germplasm name


title: plasma_control_7

source_name: peripheral blood plasma RNA, healthy donor no. 7


title: plasma_control_3

source_name: peripheral blood plasma RNA, healthy donor no. 3


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 14 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 14 days)

tag: organism part


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 21 days - rep1

tag: cell type


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 14 days - rep2

tag: development stage


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 14 days - rep1

tag: age


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 21 days - rep3

tag: growth media


title: Control. 200 DPI. Rep 2

source_name: Total RNA extracted from whole mouse brain microlgia isolated immediately after cull.  Taken at 200 dpi following innoculation with 0.02 ml of 0.02 w/v normal brain homegate (injected i.p.).


title: Nr4a1.4

city: South San Francisco

first: Josh

last: Kaminker

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

hyb_protocol: 750 ng of the labeled cRNA was fragmented and hybridized to Agilent-026655 arrays as described in manufacturer's hybridization kit.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent's Feature Extraction software was used to analyze acquired array images. Background correction of raw Agilent data was performed using the normexp function in the limma package using an offset of 50. Within-array normalization was performed using the normalizeWithinArrays function with the loess method. Last, arrays were normalized with the normalizeBetweenArrays function using the Aquantile method. Control probes were removed from the analysis. Data for duplicate probes on the Agilent array were averaged using the avereps function. Before comparison between groups, probes were filtered to ensure that only a single probe was represented for each gene using the featureFilter function with default parameters. Data were corrected for batch using sva.

source_name: cultured hippocampal neurons, Flag-Nr4a1

label_protocol: Briefly, total RNA sample was converted to double-stranded cDNA and then to Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. The labeled cRNA was purified using RNeasy mini kit (Qiagen, San Diego, CA). cRNA yield and Cy-dye incorporation were determined using ND-1000 spectrophotometer (Thermo Scientific).

extract_protocol: Total RNA was isolated using RNeasy Plus kit (Qiagen).

treatment_protocol: After 10 days in culture, dissociated mouse hippocampal neurons in 6-well plates were infected with lentivirus expressing either Flag-Nr4a1 or GFP and incubated for 6 days to allow for transgene expression.

value: hippocampal neurons

tag: transgene

tag: batch

tag: pair

source_name: Universal Mouse Reference (Stratagene, La Jolla, CA)

value: reference


title: Nr4a1.2


title: Nr4a1.3


title: Control. 200 DPI. Rep 1

tag: tissue


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 7 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 7 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 3 days - rep1

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 3 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 7 days - rep1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 3 days - rep3


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 7 days - rep2


title: Control. 100 DPI. Rep 2

source_name: Total RNA extracted from whole mouse brain microlgia isolated immediately after cull.  Taken at 100 dpi following innoculation with 0.02 ml of 0.02 w/v normal brain homegate (injected i.p.).


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 3 days - rep2


title: Control. 150 DPI. Rep 2

source_name: Total RNA extracted from whole mouse brain microlgia isolated immediately after cull.  Taken at 150 dpi following innoculation with 0.02 ml of 0.02 w/v normal brain homegate (injected i.p.).


title: Control.4

source_name: cultured hippocampal neurons, GFP

value: GFP


title: Control.3


title: Nr4a1.1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 1 days - rep1

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 1 days)

value: second order axillary bud


title: Control. 35 DPI. Rep 2

source_name: Total RNA extracted from whole mouse brain microlgia isolated immediately after cull.  Taken at 35 dpi following innoculation with with 0.02 ml of 0.02 w/v normal brain homegate (injected i.p.).


title: Control. 150 DPI. Rep 1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 28 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 28 days)


title: Control.2


title: 79A infected.  200 DPI. Rep 1

source_name: Total RNA extracted from whole mouse brain microglia isolated immediately after cull.  Taken at 200 dpi following infection with 0.02 ml of 0.02 w/v 79A strain prion disease (injected i.p.).


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 42 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 42 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 42 days - rep2


title: Control. 100 DPI. Rep 1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 1 days - rep2


title: 79A infected.  150 DPI. Rep 1

source_name: Total RNA extracted from whole mouse brain microglia isolated immediately after cull.  Taken at 150 dpi following infection with 0.02 ml of 0.02 w/v 79A strain prion disease (injected i.p.).


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 42 days - rep1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 1 days - rep3


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 28 days - rep2


title: 79A infected.  150 DPI. Rep 2


title: Control.1


title: Control. 35 DPI. Rep 1

source_name: Total RNA extracted from whole mouse brain microlgia isolated immediately after cull.  Taken at 35 dpi following innoculation with 0.02 ml of 0.02 w/v normal brain homegate (injected i.p.).


title: 79A infected.  100 DPI. Rep 1

source_name: Total RNA extracted from whole mouse brain microglia isolated immediately after cull.  Taken at 100 dpi following infection with 0.02 ml of 0.02 w/v 79A strain prion disease (injected i.p.).


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 21 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 21 days)


title: 79A infected.  200 DPI. Rep 2


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 21 days - rep1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 14 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 14 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 21 days - rep3


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 14 days - rep1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 28 days - rep1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 14 days - rep3


title: 79A infected.  35 DPI. Rep 1

source_name: Total RNA extracted from whole mouse brain microglia isolated immediately after cull.  Taken at 35 dpi following infection with 0.02 ml of 0.02 w/v 79A strain prion disease (injected i.p.).


title: arr1,10,12, dehydrated 4h, replicate 3

city: Hanoi

first: Kien

middle: Huu

last: Nguyen

state: Bac Tuliem

address: Pham Van Dong str., Bac Tuliem, Hanoi, Vietnam

department: Genetic Engineering Department

country: Viet Nam

institute: Agricultural Genetics Institute

description: Gene expression data from dehydrated arr1,10,12

hyb_protocol: 1.65 µg of Cy3-labelled cRNA were fragmented at 60°C for 30 minutes following the manufacturer's instructions. Agilent hybridization buffer was then added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarray slides were washed and dried immediately by a brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX11.5.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Arabidopsis thaliana

source_name: arr1,10,12, dehydrated 4h, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2  µg RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Two-week-old WT and arr1,10,12 mutant plants were transferred from GM plates to soil and grown for 10 additional day (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).

extract_protocol: Total RNA was extracted from the rosette leaves using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: The aerial of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0, 2 or 4h.

tag: genotype

value: arr1,10,12 mutant

value: rosette leaves

value: 24 day-old

tag: treatment

value: dehydrated 4h


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 7 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 7 days)

value: paradormancy

value: 31 days after bud break

value: peat/perlite/soil


title: arr1,10,12, dehydrated 2h, replicate 2

source_name: arr1,10,12, dehydrated 2h, replicate 2

value: dehydrated 2h


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 3 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 3 days)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 7 days - rep3


title: arr1,10,12, dehydrated 2h, replicate 3

source_name: arr1,10,12, dehydrated 2h, replicate 3


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 3 days - rep2

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/2008) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 3 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 7 days - rep1


title: 79A infected.  35 DPI. Rep 2

tag: gender

value: female


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 3 days - rep1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 1 days - rep3

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 1 day of additional LD  of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 1 days)


title: arr1,10,12, well-watered (0h), replicate 3

description: Gene expression data from well-watered arr1,10,12

source_name: arr1,10,12, well-watered, replicate 3

value: well-watered


title: arr1,10,12, well-watered (0h), replicate 1

source_name: arr1,10,12, well-watered, replicate 1


title: WT, dehydrated 4h, replicate 3

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 3

value: wild type


title: arr1,10,12, well-watered (0h), replicate 2

source_name: arr1,10,12, well-watered, replicate 2


title: arr1,10,12, dehydrated 2h, replicate 1

source_name: arr1,10,12, dehydrated 2h, replicate 1


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 1 days - rep2

value: Seyval (SV, Seyve Villard 5-276)


title: arr1,10,12, dehydrated 4h, replicate 2

source_name: arr1,10,12, dehydrated 4h, replicate 2


title: WT, dehydrated 4h, replicate 2

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 2


title: WT, dehydrated 2h, replicate 3

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 3


title: WT, dehydrated 4h, replicate 1

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 1


title: WT, dehydrated 2h, replicate 2

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 2


title: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 1 days - rep1


title: Art-/-:Nfkb2-/-:IgH:Bcl2, IL-7 wd x 2d, rep3

city: St. Louis

first: Jeffrey

middle: J

last: Bednarski

state: Missouri

address: 660 S. Euclid Ave.

department: Pediatrics

institute: Washington University School of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Gene expression levels were determined using Partek's plug-in for GenomeStudio Gene Expression Module.
GenomeStudio Gene Expression Module v2010 (Illumina) was used to compute quantile normalized, background-subtracted average signal intensity.  Data was shited by 38.33989 and log2 transformed.

source_name: Art-/-:Nfkb2-/-:IgH:Bcl2_IL-7 wd x 2d

label_protocol: Purified RNA was labeled according to manufacturer's protocol.

growth_protocol: Primary pre-B cell cultures were generated from bone marrow harvested from 4-6 week old mice and cultured for 7-10 days at 2 x 10^6 cells/mL in media containing 5 ng/mL of IL-7 (Life Technologies).  For IL-7 withdrawal experiments, cells were resuspended in media without IL-7 and maintained at 2 x 10^6 cells/mL.

extract_protocol: RNA was purified using Qiagen RNeasy Kits according to the manufacturer’s protocol.

tag: strain background

value: mixed; C57BL/6 and BALB/c

tag: tissue source

value: pre-B cells

tag: genotype/variation

tag: time point

value: 2 days after IL-7 withdrawal


title: Art-/-:IgH:Bcl2, IL-7 wd x 2d, rep3

source_name: Art-/-:IgH:Bcl2_IL-7 wd x 2d

value: bone marrow harvested from 4-6 week old mice


title: Art-/-:IgH:Bcl2, IL-7 wd x 2d, rep2


title: Art-/-:Nfkb2-/-:IgH:Bcl2, IL-7 wd x 2d, rep2


title: Art-/-:Nfkb2-/-:IgH:Bcl2, IL-7 wd x 2d, rep1


title: BPH4

city: Derio

first: Verónica

last: Torrano Moya

address: 801 Building. Technology Park of Vizcaya

country: Spain

institute: CICbioGUNE

description: uEV RNA

data_processing: The data were normalised using quantile normalisation with lumi package in R.  Probes with detection p-value < 0.01 were selected for normalization.

source_name: urine-ExtracellularVesicles (uEV) isolated by ultracentrifugation_BPH

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

growth_protocol: Urine was collected from patients, processed, uEVs were isolated by ultracentrifugation and total RNA was extracted.

extract_protocol: Rneasy columns (Qiagen, Inc)

value: urine

tag: patient diagnosis

value: BPH

tag: cell compartment

value: Extracellular Vesicles


title: BPH3

description: uEV RNA


title: Rag-/-:IgH:Bcl2, IL-7 wd x 2d, rep3

source_name: Rag-/-:IgH:Bcl2_IL-7 wd x 2d

tag: cell type


title: WT, well-watered (0h), replicate 3

description: Gene expression data from well-watered WT

source_name: WT, well-watered, replicate 3

value: rosette leaves

value: 24 day-old


title: BPH1

description: uEV RNA


title: WT, well-watered (0h), replicate 1

source_name: WT, well-watered, replicate 1


title: PCa10

description: uEV RNA

source_name: urine-ExtracellularVesicles (uEV) isolated by ultracentrifugation_Pca

value: PCa


title: WT, dehydrated 2h, replicate 1

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 1


title: Rag-/-:IgH:Bcl2, IL-7 wd x 2d, rep2


title: DUOC-01 cells_3

city: Durham

first: Arjun

last: Saha

state: NC

address: 10 circuit dr, RP2

department: DTMI

institute: Duke University School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on Human Genome U133 Plus 2.0 GeneChips (Affymetrix, Santa Clara, CA) in the Affymetrix Hybridization Oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G System.

data_processing: Partek Genomics Suite 6.6 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was done on the entire dataset.

label: Biotin

source_name: DUOC-01 cells

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA.

growth_protocol: To prepare CD14+ cells for RNA for microarray analysis, freshly collected CB units or peripheral blood from healthy adult volunteers were centrifuged on Ficoll to prepare MNC fractions. These were treated with 0.15M NH4Cl to lyse erythrocytes, washed in phosphate-buffered saline, and then incubated on ice with PeCy7-mouse anti-human CD14 (BD, cat# 562698), FITC-mouse anti-human CD3 (BD, Cat#555339) and FITC-mouse anti-human CD235a (BD, Cat#559943) antibodies. Cells were then flow sorted twice to yield CD14(+)/CD235a(-)/CD3(-) populations. The first enrichment sort was followed by a second purity sort. Cells were maintained at 0-4˚C during all procedures including flow sorting. The purity of selected populations and the extent of CD14+ cell depletion were determined by flow cytometry. DUOC-01 cells were cultured following the protocol described by Kurtzberg et al. 2015 (PMID 25770677).

extract_protocol: Total RNAs were isolated from the cells by using RNeasy kit (Qiagen, USA) following manufacturer's protocol. Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE).

value: DUOC-01 cells


title: WT, well-watered (0h), replicate 2

source_name: WT, well-watered, replicate 2


title: PCa9

description: uEV RNA


title: BPH2

description: uEV RNA


title: Rag-/-:IgH:Bcl2, IL-7 wd x 2d, rep1


title: Art-/-:Nfkb2-/-:IgH:Bcl2, in IL-7, rep3

source_name: Art-/-:Nfkb2-/-:IgH:Bcl2_in IL-7

value: 0 days (in IL-7)


title: Art-/-:IgH:Bcl2, IL-7 wd x 2d, rep1


title: Art-/-:Nfkb2-/-:IgH:Bcl2, in IL-7, rep2


title: DUOC-01 cells_1


title: DUOC-01 cells_2


title: Art-/-:Nfkb2-/-:IgH:Bcl2, in IL-7, rep1


title: Purified CD14+ cells from peripheral blood of healthy adults 4

source_name: purified CD14+ monocytes, peripheral blood

value: CD14+ monocytes

tag: tissue origin

value: Freshly isolated peripheral blood from healthy adults


title: PCa5

description: uEV RNA


title: Jmjd4 shRNA replicate 1_exon level

status: Public on Jan 12 2016

city: Worcester

first: Yu-Jie

last: Hu

state: MA

address: 55 Lake Avenue North

department: Cell & Developmental Biology

institute: UMass Medical School

description:
raw data file: shJmjd4_R1_(MoEx-1_0-st-v1).CEL available on sample GSM2037244
RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: The labled mix was hybridized to Mouse Exon 1.0 ST Arrays (Affymetrix) in the GeneChip Hybridization Oven 640 (Affymetrix) overnight at the UMass Medical School Genomic Core Facility

scan_protocol: The arrays were scanned using the GeneChip Scanner 7G (Affymetrix)

data_processing: The probe cell intesity data was processed with Affymetrix Expression Console software to generate CHP files using the Robust Multichip Analysis (RMA)-sketch algorithm workflow.

source_name: NIH3T3 cell line_Jmjd4 shRNA

label_protocol: Single-stranded cDNA was synthesized from 500 ng RNA using the Ambion WT kit (Life Technologies) and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: The NIH3T3 cells were maintained in DMEM high glucose medium containing 10% calf serum and 100U/ml penicillin/streptomycin in a humidfied incubactor with 5% CO2 at 37oC.

extract_protocol: The cells were directly lysed by using Trizol reagent (Invitrogen). Total RNA was isolated from TRIzol lysates using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The cells were transduced with lenviral vectors encoding shRNAs for 48 hrs and subsequently selected in media containing 2.5 μg/ml puromycin for 7 days.

tag: cell line

value: fibroblast


title: Jmjd4 shRNA replicate 2_exon level

description:
raw data file: shJmjd4_R2_(MoEx-1_0-st-v1).CEL available on sample GSM2037246
RMA expression value derived from Expression Console software; core-exon analysis


title: Control shRNA replicate 1_exon level

description:
raw data file: shCtrl_R1_(MoEx-1_0-st-v1).CEL available on sample GSM2037236
RMA expression value derived from Expression Console software; core-exon analysis

source_name: NIH3T3 cell line_control shRNA


title: Jmjd6 shRNA replicate 1_exon level

description:
raw data file: shJmjd6_R1_(MoEx-1_0-st-v1).CEL available on sample GSM2037240
RMA expression value derived from Expression Console software; core-exon analysis

source_name: NIH3T3 cell line_Jmjd6 shRNA


title: PCa7

description: uEV RNA


title: Purified CD14+ cells from peripheral blood of healthy adults 3


title: PCa8

description: uEV RNA


title: Purified CD14+ cells from human umbilical cord blood 4

source_name: purified CD14+ monocytes, umbilical cord blood

value: Freshly collected umbilical cord blood


title: Purified CD14+ cells from peripheral blood of healthy adults 1


title: Art-/-:IgH:Bcl2, in IL-7, rep1

source_name: Art-/-:IgH:Bcl2_in IL-7


title: Jmjd6 shRNA replicate 2_exon level

description:
raw data file: shJmjd6_R2_(MoEx-1_0-st-v1).CEL available on sample GSM2037242
RMA expression value derived from Expression Console software; core-exon analysis


title: Purified CD14+ cells from peripheral blood of healthy adults 2


title: Art-/-:IgH:Bcl2, in IL-7, rep3


title: Rag-/-:IgH:Bcl2, in IL-7, rep3

source_name: Rag-/-:IgH:Bcl2_in IL-7


title: Purified CD14+ cells from human umbilical cord blood 2


title: Rag-/-:IgH:Bcl2, in IL-7, rep2


title: Control shRNA replicate 2_exon level

description:
raw data file: shCtrl_R2_(MoEx-1_0-st-v1).CEL available on sample GSM2037238
RMA expression value derived from Expression Console software; core-exon analysis


title: 6 h safranal-treated seedlings vs control: replicate 2

city: Fuchu

first: Naoya

last: Wasano

state: Tokyo

address: Saiwai-cho 3-5-8

country: Japan

institute: Tokyo University of Agriculture & Technology

description: Biological replicate 2 of 2

hyb_protocol: Mixtures of 0.825 µg of Cy3-labeled and Cy5-labeled cRNAs were co-hybridized at 65 °C for 17 h on an Agilent Technologies 4 × 44K Arabidopsis 4 60-mer oligo-microarray.

scan_protocol: The slides were then washed and scanned with an Agilent G2505B Scanner to detect fluorescence intensity.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Data represent the log ratio control/treated). Features flagged in Feature Extraction software as non-uniform (IsFeatNonUnifOL and IsFeatPopnOL field),

source_name: 6 h safranal-treated seedlings

label_protocol: Two-color spike mix was added to the total RNA, and the RNA was labeled with a Quick Amp Labeling Kit, two-color (Agilent Technologies), according to the manufacturer’s protocol. Fluorescent cRNA was generated from total RNA: 500 ng of RNA was reverse-transcribed with MMLV reverse transcriptase and an oligo(dT) primer containing the T7 promoter, and subsequently transcribed in vitro using T7 RNA polymerase, resulting in Cy3-labeled (control) and Cy5-labeled (cis-CA-treated) cRNAs. The cRNAs were purified through RNeasy Mini Spin columns (Qiagen) and then quantified with a NanoDrop ND-1000 UV-VIS spectrophotometer

growth_protocol: The sterilized seeds were placed on 0.8% agar (Nakalai Tesque, Inc., Kyoto, Japan) with Murashige and Skoog Plant Salt Mixture (Nihon Pharmaceutical Co., Ltd., Tokyo, Japan) and 1% sucrose (Wako Pure Chemical Industries, Osaka, Japan) in a sterilized Petri dish (90-mm diameter). The seeds were held at 4 °C overnight in darkness and then transferred to a growth chamber. Emerging plants were maintained in the growth chamber under a schedule of 16-h light (22 °C) and 8-h dark (20 °C).

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

treatment_protocol: After 14 d in the growth chamber, seedlings were removed from the agar and  transferred to 20 ml of deionized water in petri-dish. Seedlings were transferred to air-tight chambers and exposed to 3.1 ppb aerial safranal for 6 h, and immediately frozen in liquid nitrogen, and then stored at –80 °C before analysis.

tag: cultivar

value: Col. 0

tag: age

value: day 14

value: seedling

source_name: control seedlings


title: Art-/-:IgH:Bcl2, in IL-7, rep2

value: mixed; C57BL/6 and BALB/c

value: pre-B cells


title: Purified CD14+ cells from human umbilical cord blood 1


title: 6 h  safranal-treated seedlings vs control: replicate1

description: Biological replicate 1 of 2


title: Rag-/-:IgH:Bcl2, in IL-7, rep1

value: bone marrow harvested from 4-6 week old mice


title: QYRC-01

city: Shanghai

first: Huang

last: Qingshan

state: Shanghai

address: No 2005, Songhu Road

department: Genetics

country: China

institute: Fudan University

description: no

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HCC cell line  QGY-7703, superinfected with H-1PV

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

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

tag: Sex

value: female

value: 35 years old

value: liver cancer


title: QY-01

description: no

source_name: HCC cell line  QGY-7703, untreated


title: VSMC_siRNA_4

city: Beijing

first: Lei

last: Yang

address: No.8 Gongtinanlu

department: Medical Research Center

institute: Beijing Chaoyang Hosptial, Capital Mediacal Unversity

hyb_protocol: 1.5 ug of Cy3-labelled cDNA  was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Adenovirus (Adv) empty vector (EC)24 hours

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA were extracted with Trizol reagents.Then, the RNA were reverse transcripted into cDNA.

treatment_protocol: Before,the human aorta vascular smooth muscle cells were washed with PBS for three time. The cells were transfected with siRNA targeting LncVSM or scrambled siRNA with Smooth Muscle Cells (ECM) media conatined 5% FBS. The media were removed and the cells were collected after 24 hours.

value: vascular smooth muscle

value: transfected with scrambled siRNA for 24 hours


title: VSMC_siRNA_3


title: VSMC_si-LncVSM_4

source_name: Adenovirus (Adv)LncVSM 24 hours

value: transfected with siRNA targeting lncVSM for 24 hours


title: VSMC_si-LncVSM_3


title: arr1,10,12, dehydrated 4h, replicate 1

source_name: arr1,10,12, dehydrated 4h, replicate 1

value: arr1,10,12 mutant

value: rosette leaves

value: 24 day-old

value: dehydrated 4h


title: VSMC_siRNA_1


title: VSMC_si-LncVSM_1


title: VSMC_siRNA_2


title: P90- Renal Medulla

city: New York City

first: Dr. Yu Leng

last: Phua

state: New York

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

description: P90- Renal Medulla

data_processing: The data were vst transformed and rsn normalised with lumi in R

source_name: P90- Renal Medulla

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

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

tag: tissue type

value: Postnatal renal medulla

tag: strain

value: male


title: P20- Renal Medulla

description: P20- Renal Medulla

source_name: P20- Renal Medulla


title: VSMC_si-LncVSM_2

tag: tissue


title: P30- Renal Medulla

description: P30- Renal Medulla

source_name: P30- Renal Medulla


title: P10- Renal Medulla

description: P10- Renal Medulla

source_name: P10- Renal Medulla


title: P8- Renal Medulla

description: P8- Renal Medulla

source_name: P8- Renal Medulla


title: C40T00602E

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

hyb_protocol: 600 ng labeled product was hybridized to slides using a NimbleGen Hybridization Kit (cat. no. 05583 934 001), then hybridized for 16 h at 42 degrees.

scan_protocol: Slides were scanned using a Roche NimbleGen MS 200 scanner and data extracted with NimbleScan v.2.6.

data_processing: Arrays were normalized using the RMA implementation of the R oligo software package (Irizarry et al. 2003)

source_name: Carcinoma

label_protocol: Total RNA (150 ng) was processed using a Low Input Quick Amp WT Labeling Kit (Agilent)

extract_protocol:
RNA from clinical samples was isolated as follows. Large RNAs (>200 bases) were isolated from fresh frozen tissue sample using RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer´s instructions. The small RNAs (<200 bases) were recovered from the flow-through fraction using RNeasy Micro Kit together with the RNeasy MinElute spin columns (Qiagen)(described in the Supplementary Material). Total RNA from cell lines harvested with Qiazol (Qiagen) was purified using miRNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
RNA extracted from fresh frozen tissue

value: Carcinoma


title: C14P00379E

source_name: Adenoma

value: Adenoma


title: C43T00731E


title: C09P00658E


title: C39N01420E

source_name: NormAdj

value: NormAdj


title: P6- Renal Medulla

description: P6- Renal Medulla

source_name: P6- Renal Medulla


title: P2- Renal Medulla

description: P2- Renal Medulla

source_name: P2- Renal Medulla


title: HT29

source_name: cell line


title: C40N01249E


title: C37P01398E


title: P4- Renal Medulla

description: P4- Renal Medulla

source_name: P4- Renal Medulla


title: PCa6

description: uEV RNA

source_name: urine-ExtracellularVesicles (uEV) isolated by ultracentrifugation_Pca

value: urine

value: PCa

value: Extracellular Vesicles


title: P30 - Renal Cortex

description: P30 - Renal Cortex

source_name: P30 - Renal Cortex

value: Postnatal renal cortex


title: P20 - Renal Cortex

description: P20 - Renal Cortex

source_name: P20 - Renal Cortex


title: P90 - Renal Cortex

description: P90 - Renal Cortex

source_name: P90 - Renal Cortex


title: P10 - Renal Cortex

description: P10 - Renal Cortex

source_name: P10 - Renal Cortex


title: P0- Renal Medulla

description: P0- Renal Medulla

source_name: P0- Renal Medulla


title: C16T00649E


title: C16T00536E


title: C40N01233E


title: P8 - Renal Cortex

description: P8 - Renal Cortex

source_name: P8 - Renal Cortex


title: C31T00260E


title: P6 -Renal Cortex

description: P6 -Renal Cortex

source_name: P6 -Renal Cortex


title: C35T00933E


title: C10P01108E


title: P4 - Renal Cortex

description: P4 - Renal Cortex

source_name: P4 - Renal Cortex


title: P2 - Renal Cortex

description: P2 - Renal Cortex

source_name: P2 - Renal Cortex


title: C43T00717E

source_name: Carcinoma


title: C13T01282E

source_name: Adenoma


title: C38T00443E


title: C32N00913E

source_name: NormAdj


title: C24T00894E


title: Replicate-1 PDGFRaH2BeGFP/Sca-

city: London

first: Ryan

middle: R

last: Driskell

address: 28th Floor Guys Tower

department: Centre for Stem Cells and Regenerative Medicine

institute: King's College London

hyb_protocol: Standard hyb protocol.

scan_protocol: Array images produced by the Affymetrix PICR 3000 scanner

data_processing: Genespring GX11 (Agilent) for analysis. RMA normalization (baseline to median of all samples) was used. Analyses were performed on genes selected for expression above the bottom 20th percentile in all three samples within at least one of two experimental groups.

label_protocol: Cells were labeled in PBS + 10% FBS TruStain fcX anti-mouse blocking buffer with the following antibodies: anti-mouse Ly-6A/E (Sca-1)-Alexa Fluor-700

extract_protocol: Over 5e5 fibroblasts of each population were isolated by flow cytometry.  Total RNA was purified from sorted cell populations using Purelink Micro Total RNA Purification System kit (Invitrogen), including an on-column DNase treatment step.

value: PDGFRAeGFP

value: P2 dermal skin

tag: cell population


title: Purified CD14+ cells from human umbilical cord blood 3

source_name: purified CD14+ monocytes, umbilical cord blood

value: CD14+ monocytes

value: Freshly collected umbilical cord blood


title: P0 - Renal Cortex

description: P0 - Renal Cortex

source_name: P0 - Renal Cortex

tag: gender


title: Replicate-2 PDGFRaH2BeGFP/Sca1+


title: C30N01597E

source_name: NormDiv

value: NormDiv


title: Replicate-3 PDGFRaH2BeGFP/Sca1+


title: Replicate-3 PDGFRaH2BeGFP/Sca-


title: C31P00913E


title: C35T01155E


title: C42T00978E


title: DLD1

source_name: cell line


title: C17T00865E


title: C27T00287E


title: C38P00960E


title: GC ImHABCL6 rep2

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

hyb_protocol: Affymetrix Mouse 430 2.0 GeneChips® at 45º C for 16 hours

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: The data were analyzed with the Partek software using  default analysis settings and RMA as normalization method.

source_name: Splenic GC B-cells

label_protocol: Affymetrix 3' IVT Express kit

growth_protocol: Following immunization with sheep red blood cells, GC B-cells were isolated from the spleens of mice using magnetic beads (according to Cato, M.H., Yau, I.W. & Rickert, R.C., 2011. Nature protocols, 6(7), pp.953–960.)

extract_protocol: RNeasy

value: Splenic GC B-cells


title: GC ImHABCL6 rep3


title: GC ImHABCL6/Uchl1 rep3


title: C10T01098E


title: GC ImHABCL6/Uchl1 rep2


title: C43T00978E


title: C41N00895E


title: GC ImHABCL6/Uchl1 rep1


title: Replicate-2 PDGFRaH2BeGFP/Sca-


title: C43T00895E


title: GC ImHABCL6 rep1


title: C25T00212E


title: Replicate-1 PDGFRaH2BeGFP/Sca1+


title: C39P01249E


title: C18T00629E


title: C22T00759E


title: C12P01103E


title: C27N00945E


title: C45N01413E


title: C38N00726E


title: C10N00935E


title: C17P01448E


title: HCT116


title: C39P01233E


title: C43P00988E


title: C23T00489E


title: C11T00781E


title: C11P01286E


title: C27N01184E


title: C44T00731E


title: C32T01065E


title: LS174T


title: C31P01151E


title: C21T00427E


title: C10P00660E


title: C12T00133E


title: DLD1 TR7

value: DLD1 TR7


title: HCT115


title: C42T00895E


title: C16T01045E


title: Normal tissue3

first: Chun-Wu

last: Pan

address: 1665 KONG JIANG ROAD

department: Department of Urology

institute: Xinhua Hospital, Shanghai Jiao Tong University School of Medicine

description: Gene expression data from normal tissues of normal SD rats.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Rattus norvegicus

source_name: Normal bladder tissue

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Female 10 weeks old SD rats were intravesical instilled of 20mg/ml MNU once per week for 10 weeks, then CT scanning confirmed that the tumors grew in bladders, and the pathologic type was bladder transitional cell carcinoma (BTCC) by H&E staining.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Tissues rinsed with PBS and placed on ice in the Trizol solution (Life technologies).

value: baldder

value: female

value: 10 weeks


title: C26T01184E


title: C32T00779E

value: Carcinoma


title: Normal tissue2


title: Adjacent normal tissue1

description: Gene expression data from adjacent normal tissues of SD rats with BTCC.

source_name: Bladder adjacent normal tissue


title: C31T00479E


title: Normal tissue1


title: BTCC tissue2

description: Gene expression data from SD rat bladder cancer tissues.

source_name: Bladder cancer tissue


title: C14T00464E


title: C23T00211E


title: SW480


title: Adjacent normal tissue2


title: Cells depleted for BRPF3, biological rep2

city: Copenhagen

first: Anja

last: Groth

address: Ole Maaløes Vej 5, DK-2200 Copenhagen N

institute: Copenhagen University

description: Gene expression data from U2OS cells treated with siRNA against BRPF3.

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized for 16 hr at 45C on Humane Genome 2.0. GeneChips followd by the wash and stain protocol on the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 30007G.

data_processing: RMA using quantile normalization.

source_name: Human osteosarcoma U2OS cells depleted for BRPF3

label_protocol: Biotin end-labeled sense cRNA was prepared using the GeneChip WT PLUS array according to the Affymetrix protocol from  250ng of total RNA (GeneChip® WT PLUS Reagent Kit, 2013, Affymetrix).

growth_protocol: U2OS cells were grown in DMEM (Gibco) containing 1% Pen/Strep and 10% FBS (Hyclone).

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with siRNAs at 50 nM (Sigma) concentration using lipofectamine RNAi MAX (Invitrogen) in accordance with to the manufacturer's instructions..

tag: treatment

value: BRPF3 depletion


title: Adjacent normal tissue3


title: BTCC tissue1


title: BTCC tissue3


title: C15T00347E


title: C21T00294E


title: C34N01373E

value: NormAdj


title: LM CD24+ fraction RA

first: Adrian

last: Biddle

address: 4 Newark Street

department: Blizard Institute

institute: Queen Mary, University of London

hyb_protocol: Standard illumina protocol

scan_protocol: Standard illumina protocol

data_processing: Quantile normalisation

source_name: human OSCC cell line

label_protocol: Standard illumina protocol

growth_protocol: Grown in FAD medium.

extract_protocol: Qiagen Rneasy kit

treatment_protocol: 0.5ng/ml TGFbeat and 5uM RA. Changed every two days for eight days.

value: LM CD24+ fraction


title: Cells depleted for BRPF3, biological rep1


title: C11P00635E

value: Adenoma


title: C20T00419E


title: Control cells, biological rep2

description: Gene expression data from U2OS cells treated with scramble siRNA.

source_name: Human osteosarcoma U2OS cells treated with negative control siRNA

value: control


title: iNC-01-4_CD45+

city: Bethesda

first: Colin

middle: L

last: Sweeney

state: MD

address: Building 10-CRC, Room 5-3888, 10 Center Drive

department: NIAID - Genetic Immunotherapy Section

institute: NIH

data_processing:
Data analysis was performed using ExpressionSuite software (Applied Biosystems) for comparative CT analysis normalized to U6 snRNA and RNU48 control RNAs relative to expression in undifferentiated iPSCs, to obtain RQ values (ddCt method) for each group (iPSC, EB, CD34+, CD34+CD45+, CD45+).
The Applied Biosystems ExpressionSuite software used for analysis of this miRNA array computes a mean Ct for each group of replicate samples prior to making dCt calculations, and reports a mean RQ value for the entire group (with associated p value, RQ max, and RQ min for each group). As a result, for each miRNA all of the replicate samples within a group will have identical dCt matrix values (which the software refers to as "dCt  mean") and identical RQ matrix values. So, samples 1-5 (the iPSC cell group), samples 6-7 (the EB cell group), samples 8-10 (the CD34+CD45- cell group), samples 11-13 (the CD34+CD45+ cell group), and samples 14-16 (the  CD34-CD45+ cell group) each have identical matrix values within that  group. This method is the only analysis option available with this software, which was designed by Applied Biosystems for use with their miRNA array.

label: FAM

source_name: iNC-01-4 induced pluripotent stem cell line, differentiated, day 22, sorted CD34-CD45+

label_protocol: MicroRNA cDNA was synthesized from total RNA using TaqMan MicroRNA Reverse Transcription Kit with Megaplex RT primers (pool A and B), followed by two unbiased preamplification reactions (Megaplex PreAmp primers pool A and B; Applied Biosystems).

extract_protocol: Total RNA was purified using mirVana miRNA Isolation Kit (Applied Biosystems).

value: CD34-CD45+ cells

tag: differentiation status


title: Epi-P untreated

value: Epi-P


title: LM parental line

value: LM parental line


title: LM CD24+ fraction control


title: iNC-01-3_CD45+_rep2

source_name: iNC-01-3 induced pluripotent stem cell line, undifferentiated, day 0


title: LM CD24+ fraction TGFbeta


title: Control cells, biological rep1


title: LM CD24+ fraction TGFbeta+RA


title: pEMT-S untreated

value: pEMT-S untreated


title: pEMT-P RA

value: pEMT-P


title: C51N00946E


title: C41P01177E


title: pEMT-P TGFbeta+RA


title: pEMT-P TGFbeta


title: CA1 parental line #2

value: CA1 parental


title: iNC-01-3_CD45+_rep1


title: iNC-01-3_CD34+CD45+_rep2

value: CD34+CD45+ cells


title: iNC-01-4_CD34+CD45+


title: iNC-01-3_CD34+CD45+_rep1


title: iNC-01-3_CD34+_rep2

value: CD34+CD45- cells


title: iNC-01-4_CD34+


title: C17T00524E


title: iNC-01-3_CD34+_rep1


title: Slide 185173

city: Groningen

first: Ana

last: Solopova

address: Nijenborgh 7

department: MolGen

country: Netherlands

institute: RUG

description: Sample 1

hyb_protocol: cDNA of concentration 200ng/µL with label incorporation of at least 1pmol/µL was used for hybridization. Samples were incubated at 94°C for 2 min. Preheated (68°C) Hybridization buffer was added and the whole sample incubated for 5 min at 68°C. Then 40µL of the sample was loaded on the microarray slide and hybridised at 45°C in the hybridization oven overnight.

scan_protocol: Slides were scanned using GenePix 4200 slide scanner using 10µm resolution

data_processing: Slide images were analyzed using ArrayPro 4.5 (Media Cybernetics Inc., Silver Spring, MD). Processing and normalization (LOWESS spot pin based) of slides were done with MicroPrep software

organism: Lactococcus lactis

source_name: Net{A}, wild-type

label_protocol: Amino allyl labelled cNA was purified using NucleoSpin extract II columns and Cy3 or Cy5 dyes were incorporated at pH 9.0

growth_protocol: Cells were grown to OD600 of 0.2 in rich GM17 medium

extract_protocol: Total RNA was extracted using Roche RNA isolation kit. 10-20 µg of total RNA was mixed with random nonamers and amino allyl-dUTP/nucleotide mix, Superscript III reverse transcriptase and the buffer was added to the reaction mix. Reaction was performed in 42°C for 16 hours.

tag: genotype/variation

value: wild-type

source_name: Net{B}, mutant

value: mutant


title: iNC-01-4_EB

source_name: iNC-01-4 induced pluripotent stem cell line, differentiated, day 18

value: embryoid bodies

value: day 18 embryoid body


title: iNC-01-3_EB

source_name: iNC-01-3 induced pluripotent stem cell line, differentiated, day 22, sorted CD34+CD45-


title: pEMT-P control


title: C20T00348E

source_name: Carcinoma

value: Carcinoma


title: C33N01065E

source_name: NormAdj

value: NormAdj


title: C25T00412E


title: iNC-01-4_iPSC_rep1

source_name: iNC-01-4 induced pluripotent stem cell line, undifferentiated, day 0

value: induced pluripotent stem cells

value: day 0 undifferentiated


title: iNC-01-4_iPSC_rep2


title: pEMT-S

treatment_protocol: No treatment

value: post-EMT


title: C32N01151E


title: C28T00430E


title: pEMT-P


title: Epi-P

value: epithelial


title: Epi-S


title: C18T00724E


title: C26T00945E

source_name: Adenoma

value: Adenoma


title: C19N01417E

source_name: NormDiv

value: NormDiv


title: C39N00960E


title: CA1 parental line

value: parental


title: C50N01011E


title: C09P01121E


title: iNC-01-3_iPSC_rep2

source_name: iNC-01-3 induced pluripotent stem cell line, differentiated, day 18


title: iNC-01-3_iPSC_rep3


title: iNC-01-3_iPSC_rep1


title: C18T00763E


title: C09P00674E


title: C38P01420E


title: C19T00584E


title: C17P00908E


title: C16T01218E


title: C52T00946E


title: C20T00977E


title: LS174T TR4

source_name: cell line

value: LS174T TR4


title: C12P00769E


title: SW620


title: C13P01174E


title: C25N00395E


title: C17T00654E


title: C09P00880E


title: C10P00965E


title: Tendon fibroblasts treated with PRP, replicate 2

city: Ann Arbor

first: Christopher

last: Mendias

state: MI

address: BSRB 2017, 109 Zina Pitcher Pl

department: Orthopaedic Surgery

institute: University of Michigan

description: Gene expression data from tendon fibroblasts treated with PRP

hyb_protocol: Following fragmentation, 2.8 ug of cDNA were hybridized for 20 hr at 48C on Rat Gene ST 2.1 strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical environment version 3.1.1. RMA was used to fit normalized log2 transformed expression values.

source_name: Tendon fibroblasts treated with PRP

label_protocol: cDNA were prepared according to the NuGen WT-Pico V2 kit protocol from 15 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared from 3 ug of cDNA (Encore Biotin Module P/N 4200).

growth_protocol: Tendon fibroblasts were maintained in growth media consisting of DMEM plus 10% fetal bovine serum plus 1% antibiotic/antimycotic.

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

treatment_protocol: After 2 days, growth media was changed to DMEM plus 1% antibiotic/antimycotic plus 10% PRP or PPP clot releasate.

value: Tail tendon

tag: genotype

value: Lewis

value: Retired breeders


title: 23_Sc Galactose MDM33 downtags repl2

city: Bayreuth

first: Alfons

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

country: Germany

institute: University of Bayreuth

description: locus: downtags

hyb_protocol: Labelled Uptag and Downtag samples were incubated with blocking oligonucleotides as described in Pan et al. (2007) dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods 41(2): 206–221. Hybridization was carried out at 50°C using Agilent's blocking agent and Hi-RPM buffer; slides were washed using Agilent's Oligo aCGH Wash Buffer 1 and 2. Cyanine dye decomposition was inhibited using Agilent's Stabilization and Drying solution.

scan_protocol: Slides were scanned on a FLA8000 microarray scanner (Fujifilm) at 5 µm resolution in confocal mode.

data_processing: Spot intensities were calculated as 'median-trimmed mean densities', background intensities were calculated from selected spot groups ('dark corners' in the Agilent array) and used to correct spot intensities; the raw data of each Cy3 and Cy5 channels were normalized to a value of 147,680,000 (total intensity normalization);

organism: Saccharomyces cerevisiae

source_name: plate cultures

label_protocol: Uptag and Downtag sequences were amplified and labelled by asymmetric PCR as described in Pan et al. (2007) dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods 41(2): 206–221;

growth_protocol: The pooled collection of deletion strains was grown in rich media (2% glucose, 2% peptone, 1% yeast extract) to middle-log phase. The pool was transformed with either pYX223 or pYX223-MDM33 using the LiAc/PEG method and after transformation the cells were plated on solid selection media (2% agar, 2% glucose, 0.67 % yeast nitrogen base without amino acids, 30 mg / l L-leucine, 30 mg / l L-lysine, 20 mg / l uracil). After 4 days of incubation at 30°C, transformants were washed off the plates with sterile 1x PBS. The pooled transformants were then plated on selective media (2% agar, 0.67 % yeast nitrogen base without amino acids, 30 mg / l L-leucine, 30 mg / l L-lysine, 20 mg / l uracil) containing either 2% glucose or 2% galactose. After 2 (glucose) or 4 (galactose) days of incubation at 30°C cells were washed off the agar plates with sterile 1xPBS.

extract_protocol: Genomic DNA was extracted using the 'NucleoMag 96 Plant' DNA isolation kit (Machery-Nagel, Dueren, Germany)

treatment_protocol: Cells were grown either on media containing 2% glucose (control condition) or 2% galactose (induction of MDM33 overexpression).

tag: knockout collection

value: YSC1054 Open Biosystems

tag: plasmid

tag: carbon source

value: Galactose


title: 25_Sc Glucose empty uptags repl2

description: locus: uptags

value: Glucose


title: Colo205


title: 21_Sc Galactose MDM33 uptags repl2

description: locus: uptags


title: Tendon fibroblasts treated with PPP, replicate 2

description: Gene expression data from tendon fibroblasts treated with PPP

source_name: Tendon fibroblasts treated with PPP


title: Tendon fibroblasts treated with PPP, replicate 1


title: 24_Sc Glucose empty downtags repl2

description: locus: downtags


title: Tendon fibroblasts treated with PRP, replicate 1


title: 20_Sc Galactose empty uptags repl2

description: locus: uptags


title: 19_Sc Galactose empty downtags repl2

description: locus: downtags


title: C19T00755E


title: C33T01373E


title: C36N01155E


title: Jmjd4 shRNA replicate 2_gene level

description: RMA expression value derived from Expression Console software; core-gene analysis

source_name: NIH3T3 cell line_Jmjd4 shRNA

tag: cell type

value: fibroblast