title: Cell-Knockout-Rep3

first: Wenxi

last: Yu

state: N/A = Not Applicable

address: No.600, Yishan Road, Xuhui District, 200233 Shanghai, People's Republic of China

institute: Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University

description: Synovial sarcoma, Female,Whilte,25 years old

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA 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: SW982 cells treated with GINS1 silencing

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

growth_protocol: SW982 cells were maintained in T-150 flasks (Corning, Tewksbury,MA, USA) in RPMI-1640 medium containing 2 mM L-glutamine,10% fetal bovine serum and 1% Pen-Strep at 37 °C, 5% CO2

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

treatment_protocol: SW982 cells were treated with or without GINS1 knockdown and investigated by a microarray profiling

tag: cell line

tag: genotype/variation

value: with GINS1 silencing


title: human Tregs_unstimulated_NRP1-KD_2

status: Public on Jan 01 2019

type: RNA

city: Oxford

first: Ruud

last: van Stiphout

address: Old Road Campus Research Building

country: United Kingdom

institute: University of Oxford

description: Sample 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with R-package LIMMA (normalizeQuantiles)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human peripheral blood

label_protocol: biotinylation

growth_protocol: 16-day Treg expansion protocol with anti-CD3/anti-CD28 beads and interleukin-2 (see Hester et al (2012) Low‐Dose Rapamycin Treatment Increases the Ability of Human Regulatory T Cells to Inhibit Transplant Arteriosclerosis In Vivo. American Journal of Transplantation).

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini kit

treatment_protocol: lentivirus-mediated transduction with pLKO1 vector (TRC consortium) encoding either shRNA against NRP1 (human neuropilin-1 gene) or scrambled control

tag: cell type

value: Tregs

tag: shRNA

tag: biological replicate (donor)

tag: stimulation condition

value: 72hrs no beads

tag: cell subtype


title: human Tregs_unstimulated_NRP1-KD_1

description: Sample 2


title: human Tregs_unstimulated_control vector pLKO1_1

description: Sample 1

value: control


title: Cell-Knockout-Rep1

city: Shanghai

country: China


title: human Tregs_unstimulated_control vector pLKO1_2

description: Sample 3


title: human Tregs_unstimulated_NRP1-KD_3

description: Sample 8


title: Cell-Knockout-Rep2


title: human Tregs_stimulated_NRP1KD_1

description: Sample 6

value: 72hrs with anti-CD3/anti-CD28 beads & IL-2


title: Cell-control-Rep2

source_name: SW982 cells treated without GINS1 silencing

value: without GINS1 silencing


title: Cell-control-Rep3


title: Cell-control-Rep1


title: Cell-Control-Rep3

source_name: SW982 cells treated without anlotib as control

treatment_protocol: SW982 cells were treated with anlotib(10μM/ml) and investigated by a microarray profiling

tag: agent


title: no_melanoma [6264550114_R03C01]

type: genomic

city: Barcelona

first: joan anton

last: Puig Butille

address: Villarroel 170

country: Spain

institute: Hospital Clínic

description: individual belonging to a melanoma-prone family who has not developed melanoma

hyb_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html

data_processing:
Germline genomic DNA was genotyped using HumanOmni2.5-8v1 Genotyping BeadChips (Illumina). The .idat files were processed using the Genotyping Module of the GenomeStudio 2011.1 software package (Illumina Inc., San Diego CA 92122, U.S.A.) with default settings according to the manufacturer's user guide. The required manifest and cluster files were downloaded from http://support.illumina.com/array/downloads.html.
Genotype: AA,AB,BB,or NC (no call)

label: Cy5, Cy3

molecule: genomic DNA

extract_protocol: Germline genomic DNA was extracted from blood samples using the salting out method or saliva samples using DNA Genotek kits

tag: subject status

tag: ethnicity

value: Caucasian

tag: gender

value: female

tag: subject group

tag: tissue

value: blood


title: Cell-Control-Rep1


title: Cell-Control-Rep4


title: no_melanoma [6264550112_R05C01]

scan_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html

value: individual belonging to a melanoma-prone family who has not developed melanoma


title: no_melanoma [6264550112_R06C01]

label_protocol: Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html

value: male


title: no_melanoma [6264550112_R02C01]


title: Cell-Drug-Rep3

source_name: SW982 cells treated with anlotib(10μM/ml)


title: Infected with NTC shRNAs 01

city: Heidelberg

first: Mikolaj

last: Slabicki

address: Im Neuenheimer Feld 460

department: Deptartment of Translational Oncology

country: Germany

institute: German Cancer Research Center

description: shRNA

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: Chipster

source_name: Raji cell line

label_protocol: Standard Illumina protocol.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) with on-column DNase I (Qiagen) digestion. Quality control was performed with Bioanalyser.

value: Raji


title: Infected with shRNAs targeting MBD2 C 01

description: shRNA


title: no_melanoma [6264550107_R06C01]

description: individual belonging to a melanoma-prone family who has not developed melanoma, but with diagnostic of other cancer


title: melanoma_patient [6264550102_R03C01]

description: melanoma patient belonging to a melanoma-prone family


title: Infected with shRNAs targeting MBD2 C 02

description: shRNA


title: Infected with NTC shRNAs 02

description: shRNA


title: no_melanoma [6264550097_R04C01]


title: no_melanoma [6264550097_R02C01]


title: Infected with shRNAs targeting MBD2 A 02

description: shRNA


title: no_melanoma [6264550097_R01C01]


title: Cell-Drug-Rep2


title: Infected with shRNAs targeting MBD2 A 01

description: shRNA


title: no_melanoma [6264550100_R06C01]

value: individual belonging to a melanoma-prone family who has not developed melanoma, but with diagnostic of other cancer


title: no_melanoma [6264550100_R08C01]


title: Infected with shRNAs targeting MS4A1 C

description: shRNA


title: Cell-Drug-Rep1


title: no_melanoma [6264550100_R05C01]


title: no_melanoma [6264550100_R04C01]


title: IH69_THC-SIV

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

country: USA

institute: Southwest National Primate Research Center

description:
IH69
Gene expression in colonic epithelium during chronic SIV infection.

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Rhesus Macaque Genome Oligo Microarray (4 x 44K, Agilent Technologies) in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After washing the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 12 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Pathway analysis and GO Analysis were applied to determine the roles of these differentially expressed genes played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable gene expression profiling among samples.

organism: Macaca mulatta

source_name: Colon

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

extract_protocol: Total RNA was extracted using the miRNeasy mini kit from Qiagen Inc.

treatment_protocol: Twelve Indian rhesus macaques were infected intravenously with 100TCID50 dose of SIVmac251. Out of these, seven received vehicle and five were treated with delta-9-tetrahydrocannabinol. Four animals served as uninfected controls.

value: Colon

tag: infection

value: Simian immunodeficiency virus (SIV)

tag: treatment

value: Delta-9-tetrahydrocannabinol (THC)


title: IA83_THC-SIV

description:
IA83
Gene expression in colonic epithelium during chronic SIV infection.


title: melanoma_patient [6264550100_R03C01]

value: melanoma patient belonging to a melanoma-prone family


title: no_melanoma [6264550086_R01C01]


title: Infected with shRNAs targeting CREM A

description: shRNA


title: GV60_THC-SIV

description:
GV60
Gene expression in colonic epithelium during chronic SIV infection.


title: HB31_VEH-SIV

description:
HB31
Gene expression in colonic epithelium during chronic SIV infection.

value: Vehicle


title: Infected with NTC shRNAs

description: shRNA

value: shNTC


title: Infected with shRNAs targeting CREM B

description: shRNA


title: GH25_VEH-SIV

description:
GH25
Gene expression in colonic epithelium during chronic SIV infection.


title: HT48_THC-SIV

description:
HT48
Gene expression in colonic epithelium during chronic SIV infection.


title: FT11_VEH-SIV

description:
FT11
Gene expression in colonic epithelium during chronic SIV infection.


title: melanoma_patient [6264550075_R08C01]


title: Infected with shRNAs targeting MS4A1 B

description: shRNA


title: A2L0694_THC-SIV

description:
A2L0694
Gene expression in colonic epithelium during chronic SIV infection.


title: no_melanoma [6264550075_R07C01]


title: HD08-90D_VEH-SIV

description:
HD08-90D
Gene expression in colonic epithelium during chronic SIV infection.


title: GA19_VEH-SIV

description:
GA19
Gene expression in colonic epithelium during chronic SIV infection.


title: Infected with shRNAs targeting MS4A1 A

description: shRNA


title: no_melanoma [6264550075_R06C01]


title: HV48_VEH-SIV

description:
HV48
Gene expression in colonic epithelium during chronic SIV infection.


title: no_melanoma [6264550075_R05C01]


title: IH96_VEH-SIV

description:
IH96
Gene expression in colonic epithelium during chronic SIV infection.


title: melanoma_patient [6264550042_R01C01]


title: KO_trg2

type: SRA

city: Basel

first: Geoffrey

last: Fucile

address: Klingelbergstrasse 50/70

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

library_source: transcriptomic

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to the GRCm38 genome using STAR v1.7.20 in 2-pass mode. Read counts were generated using the --quantMode GeneCounts flag.
Genome_build: GRCm38

molecule: polyA RNA

organism: Mus musculus

source_name: Murine regulatory T cells

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Murine regulatory T cells

tag: genotype


title: KO_trg1


title: no_melanoma [6264550007_R06C01]


title: melanoma_patient [6264550007_R04C01]


title: HT22_Uninfected

description:
HT22
Gene expression in colonic epithelium of uninfected rhesus macaque.

value: Uninfected

value: Untreated


title: no_melanoma [6264550007_R03C01]


title: WT_trg3

value: WT


title: KO_trg3


title: EH70_Uninfected

description:
EH70
Gene expression in colonic epithelium of uninfected rhesus macaque.


title: EL66_Uninfected

description:
EL66
Gene expression in colonic epithelium of uninfected rhesus macaque.


title: WT_trg1


title: EH80_Uninfected

description:
EH80
Gene expression in colonic epithelium of uninfected rhesus macaque.


title: no_melanoma [6264550007_R02C01]

description: individual belonging to a melanoma-prone family who has not developed melanoma

value: Caucasian


title: no_melanoma [6264550007_R01C01]


title: WT_trg2


title: KO_con3

source_name: Murine conventional T cells

value: Murine conventional T cells


title: WT_con3


title: KO_con1


title: 495V_TBP

city: Geneva

first: Slawomir

last: Kubik

address: quai Ernest-Ansermet 30

department: Molecular Biology Department

institute: University of Geneva

library_source: genomic

data_processing:
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For nucleosome occupancy tracks each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
For ChEC-seq experiments the mapped reads were extended by 1 bp only to indicate cut sites and then, the signal for each protein tested was normalized to the signal of free MNase using a Bayesian approach
For ChIP-seq the reads were shifted by 150 bp and extended by 50 bp
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

organism: Saccharomyces cerevisiae

source_name: whole organism

extract_protocol: ChIP-seq ibraries were prepared according to manufactrer's instructions (Illumina)

treatment_protocol: no rapamycin/auxin

tag: strain

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 SPT15-FLAG-HphMX ISW2-FRB-HIS3MX; INO80-aid*-9myc-HphNT Padh1-Os.TIR1

tag: antibody

value: ANTI-FLAG M2 (Sigma F3165)


title: WT_con2


title: WT_con1


title: 495R_TBP

treatment_protocol: 60 minutes rapamycin 30 minutes auxin


title: 474R_TBP

treatment_protocol: 60 minutes rapamycin

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 CHD1-FRB-KanMX; SPT15-13xmyc-KanMX

value: Anti-Myc (homemade)


title: KO_con2


title: 474V_TBP

treatment_protocol: no rapamycin


title: 474R_Pol

value: Anti-RNA polymerase II CTD repeat YSPTSPS (Abcam ab5131)


title: Empty vector2 control organoids cultured 5 months and further grown in full medium for 3 weeks

city: BALTIMORE

first: hari

last: easwaran

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

institute: Johns Hopkins University

description:
BRAF2_EV
Exome analysis
processed data file: Exon_seq_results.xlsx

data_processing:
Library strategy: Exome-seq
Potential somatic single nucleotide variants (SNVs) and small insertion/deletions in BrafCA-IND & BrafEV-12m/14m samples were identified using Varscan (v2.3.9) (Koboldt et al., 2012), and the matched BrafEV samples were used as normal control. From the result, somatic mutations were identified based on the following major criteria: (1) high mapping quality bases (read mapping quality ≥30); (2) mutations should not be significantly enriched within 5 bp of the 5′ or 3′ ends of the read; (3) there should be a significant allele frequency change (somatic_p_value <0.05); (4) the variant reads in BrafEV samples should be less than 2, and the variant reads in BrafCA-IND and BrafEV-12m/14m samples should be larger than 5. ANNOVAR was used to annotate confident variant results (Yang and Wang, 2015).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Exon_seq_results.xlsx: Potential somatic single nucleotide variants (SNVs) and small insertion/deletions in Braf_Base and BrafEV-12m/14m samples were identified using Varscan (v2.3.9), and the matched BrafEV samples were used as normal control. As shown in Exon_seq_results.xlsx, the identified somatic single nucleotide variants (SNVs) and small insertion/deletions in BRAF1_Base/BRAF2_Base/BRAF3_Base/BRAF1_EV_12m/BRAF3_EV_14m were listed. We only presented the Missense mutations, Nonsense mutations, and Frameshift mutations. The p-value were calculated by Varscan to represent the significance of allele frequency change. Also, when the mutations hit the frequent mutated genes in COSMIC cancer database, we also annotated them.

source_name: organoid culture

growth_protocol: Male mice from each genotype around the age of 40 days were euthanized by Carbon Dioxide. The first 2.5cm of proximal colon is collected from the mice. The colon crypts were isolated and the culture was established as described previously. Organoids were plated within Matrigel (Corning #356231). Culture media was made of 50% of Wnt3a conditioned media, 20% of R-Spondin conditioned media, 20% of Advanced DMEM/F12 (ThermoFisher #12634010) with B27® (ThermoFisher #17504044), 10% of Noggin conditioned media and EGF. The conditioned media for Wnt3a, R-Spondin and Noggin were made as described previously. A total of 0.5 million cells were injected subcutaneously in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) (JAX™) with Matrigel. Injection sites were examined every week for tumor growth.

extract_protocol:
DNA was extracted from cells and xenograft tissues was extract using Allprep kit mini or micro (Qiagen).
Fragmented genomic DNA was used for Illumina TruSeq library construction. Paired-end sequencing, resulting in 100 or 150 bases from each end of the DNA fragments for the exome or targeted sequencing libraries, respectively, was performed using Illumina HiSeq 2000/2500 instrumentation.

tag: strain/background

tag: genotype/variation

value: Control

value: Male

value: Proximal colon-derived cultured organoid

tag: culture time

value: 5 months

tag: culture medium

value: Full for 3 weeks


title: BRAF1 organoids cultured 5 months and further grown in Base medium for 3 weeks

description:
BRAF1_Base
Exome analysis
processed data file: Exon_seq_results.xlsx

value: Cre-activated BrafV600E

value: Base for 3 weeks


title: Empty vector1 control organoids cultured 5 months and further grown in full medium for 3 weeks

description:
BRAF1_EV
Exome analysis
processed data file: Exon_seq_results.xlsx


title: BRAF2 organoids cultured 5 months and further grown in Base medium for 3 weeks

description:
BRAF2_Base
Exome analysis
processed data file: Exon_seq_results.xlsx


title: 495V_Pol


title: 474V_Pol


title: Empty vector3 control organoids cultured 5 months and further grown in full medium for 3 weeks

description:
BRAF3_EV
Exome analysis
processed data file: Exon_seq_results.xlsx


title: 254706910156_b3 - 5B_mtsf1_before transfert_2 vs 6B_mtsf1_12h after transfert_2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: How does inhibition of CI enhance organogenesis?

hyb_protocol: 6B_mtsf1_12h after transfert_2 Cy5 / 5B_mtsf1_before transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Arabidopsis thaliana

source_name: 6B_mtsf1_12h after transfert_2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: cell culture/primary cell - Media: Arabidopsis gelled medium  Hygrometry: 70% Temperature: 21 °C Light: 10h day / 12h night

extract_protocol: 6B_mtsf1_12h after transfert_2:4.5mg. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:12h after transfert - time course study - growth conditions,time:time 12hour .

tag: sample type

value: Arabidopsis thaliana (columbia)  mutant (mutant) - harvest date:23-07-17

source_name: 5B_mtsf1_before transfert_2

growth_protocol: cell culture/primary cell - Media: Arabidopsis liquid medium  Hygrometry: 70% Temperature: 21 °C Light: 10h day / 12h night

treatment_protocol: no treatment


title: 254706910156_b4 - 6B_mtsf1_12h after transfert_2 vs 5B_mtsf1_before transfert_2

hyb_protocol: 5B_mtsf1_before transfert_2 Cy5 / 6B_mtsf1_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 495R_Pol


title: 491R_Pol

treatment_protocol: 30 minutes auxin (3-IAA)

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 SPT15-FLAG-HphMX; ISW1-aid*-9myc-HphNT Padh1-Os.TIR1


title: W90S

city: Daqing

first: Jiang

last: Zhu

state: Hei Longjiang

address: Xinyang Road 39, Gaoxin District

institute: Daqing Branch of Harbin Medical University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genomes using the Illumina Genome Analyzer Pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: intestinal

extract_protocol:
Flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: intestinal

value: wild type


title: BRAF3 organoids cultured 5 months and further grown in Base medium for 3 weeks

description:
BRAF3_Base
Exome analysis
processed data file: Exon_seq_results.xlsx


title: 491V_Pol

treatment_protocol: no auxin


title: W83S


title: 423R_TBP

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ISW2-FRB-HIS3MX; SPT15-13xmyc-KanMX


title: 254706910156_b2 - 6A_mtsf1_12h after transfert_1 vs 5A_mtsf1_before transfert_1

hyb_protocol: 5A_mtsf1_before transfert_1 Cy5 / 6A_mtsf1_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 5A_mtsf1_before transfert_1

source_name: 6A_mtsf1_12h after transfert_1

extract_protocol: 6A_mtsf1_12h after transfert_1:4.5mg. (Qiagen_RNeasy.pdf)


title: 491V_TBP


title: 491R_TBP


title: 423R_Pol


title: K82S

value: alk-SMase knockout


title: 423V_Pol


title: 423V_TBP


title: K86S


title: 501V_high

extract_protocol: Libraries were prepared essentially as described in Henikoff et al., 2011 (GSE30551) (PMID: 22025700)

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX ISW2-FRB-HIS3MX; INO80-aid*-9myc-HphNT CHD1-FRB-KanMX; ISW1-aid*-9myc-HphNT Padh1-Os.TIR1


title: K79S


title: W89S


title: 487V_high

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ISW2-FRB-HIS3MX; INO80-aid*-9myc-HphNT CHD1-FRB-KanMX; ISW1-aid*-9myc-HphNT Padh1-Os.TIR1


title: 254706910150_b2 - 6A_mtsf1_12h after transfert_1 vs 4A_WT_12h after transfert_1

hyb_protocol: 4A_WT_12h after transfert_1 Cy5 / 6A_mtsf1_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 4A_WT_12h after transfert_1

extract_protocol: 4A_WT_12h after transfert_1:4.5mg. (Qiagen_RNeasy.pdf)

value: Arabidopsis thaliana (columbia)  - harvest date:23-07-17


title: 254706910150_b3 - 4B_WT_12h after transfert_2 vs 6B_mtsf1_12h after transfert_2

hyb_protocol: 6B_mtsf1_12h after transfert_2 Cy5 / 4B_WT_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 4B_WT_12h after transfert_2

growth_protocol: cell culture/primary cell - Medium: Arabidopsis gelled medium Hygrometry: 70% Temperature: 21 °C Light: 10h day / 12h night

extract_protocol: 4B_WT_12h after transfert_2:4.5mg. (Qiagen_RNeasy.pdf)


title: 254706910156_b1 - 5A_mtsf1_before transfert_1 vs 6A_mtsf1_12h after transfert_1

hyb_protocol: 6A_mtsf1_12h after transfert_1 Cy5 / 5A_mtsf1_before transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 487R_low


title: 487V_low


title: 254706910150_b1 - 4A_WT_12h after transfert_1 vs 6A_mtsf1_12h after transfert_1

hyb_protocol: 6A_mtsf1_12h after transfert_1 Cy5 / 4A_WT_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910150_b4 - 6B_mtsf1_12h after transfert_2 vs 4B_WT_12h after transfert_2

hyb_protocol: 4B_WT_12h after transfert_2 Cy5 / 6B_mtsf1_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910149_b3 - 3B_WT_before transfert_2 vs 5B_mtsf1_before transfert_2

hyb_protocol: 5B_mtsf1_before transfert_2 Cy5 / 3B_WT_before transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 3B_WT_before transfert_2

growth_protocol: cell culture/primary cell - Medium: Arabidopsis liquid medium Hygrometry: 70% Temperature: 21 °C Light: 10h day / 12h night


title: 254706910149_b2 - 5A_mtsf1_before transfert_1 vs 3A_WT_before transfert_1

hyb_protocol: 3A_WT_before transfert_1 Cy5 / 5A_mtsf1_before transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 3A_WT_before transfert_1


title: 487R_high


title: 254706910148_b4 - 4B_WT_12h after transfert_2 vs 3B_WT_before transfert_2

hyb_protocol: 3B_WT_before transfert_2 Cy5 / 4B_WT_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 468R_high

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX ISW2-FRB-HIS3MX; INO80-aid*-9myc-HphNT Padh1-Os.TIR1


title: 254706910149_b1 - 3A_WT_before transfert_1 vs 5A_mtsf1_before transfert_1

hyb_protocol: 5A_mtsf1_before transfert_1 Cy5 / 3A_WT_before transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910147_b4 - 2B_mtl1_12h after transfert_2 vs 4B_WT_12h after transfert_2

hyb_protocol: 4B_WT_12h after transfert_2 Cy5 / 2B_mtl1_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 2B_mtl1_12h after transfert_2

extract_protocol: 2B_mtl1_12h after transfert_2:4.5mg. (Qiagen_RNeasy.pdf)


title: 254706910149_b4 - 5B_mtsf1_before transfert_2 vs 3B_WT_before transfert_2

hyb_protocol: 3B_WT_before transfert_2 Cy5 / 5B_mtsf1_before transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 468R_low


title: 254706910147_b1 - 4A_WT_12h after transfert_1 vs 2A_mtl1_12h after transfert_1

hyb_protocol: 2A_mtl1_12h after transfert_1 Cy5 / 4A_WT_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 2A_mtl1_12h after transfert_1

extract_protocol: 2A_mtl1_12h after transfert_1:4.5mg. (Qiagen_RNeasy.pdf)


title: 254706910148_b1 - 3A_WT_before transfert_1 vs 4A_WT_12h after transfert_1

hyb_protocol: 4A_WT_12h after transfert_1 Cy5 / 3A_WT_before transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 468V_low


title: 254706910148_b2 - 4A_WT_12h after transfert_1 vs 3A_WT_before transfert_1

hyb_protocol: 3A_WT_before transfert_1 Cy5 / 4A_WT_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910146_b3 - 1B_mtl1_before transfert_2 vs 2B_mtl1_12h after transfert_2

hyb_protocol: 2B_mtl1_12h after transfert_2 Cy5 / 1B_mtl1_before transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 1B_mtl1_before transfert_2


title: 254706910147_b2 - 2A_mtl1_12h after transfert_1 vs 4A_WT_12h after transfert_1

hyb_protocol: 4A_WT_12h after transfert_1 Cy5 / 2A_mtl1_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910146_b1 - 1A_mtl1_before transfert_1 vs 2A_mtl1_12h after transfert_1

hyb_protocol: 2A_mtl1_12h after transfert_1 Cy5 / 1A_mtl1_before transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 1A_mtl1_before transfert_1


title: 254706910147_b3 - 4B_WT_12h after transfert_2 vs 2B_mtl1_12h after transfert_2

hyb_protocol: 2B_mtl1_12h after transfert_2 Cy5 / 4B_WT_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 452R_high

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX INO80-aid*-9myc-HphNT Padh1-Os.TIR1


title: 254706910148_b3 - 3B_WT_before transfert_2 vs 4B_WT_12h after transfert_2

hyb_protocol: 4B_WT_12h after transfert_2 Cy5 / 3B_WT_before transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 468V_high


title: 254706910146_b4 - 2B_mtl1_12h after transfert_2 vs 1B_mtl1_before transfert_2

hyb_protocol: 1B_mtl1_before transfert_2 Cy5 / 2B_mtl1_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 452V_high


title: 254706910146_b2 - 2A_mtl1_12h after transfert_1 vs 1A_mtl1_before transfert_1

hyb_protocol: 1A_mtl1_before transfert_1 Cy5 / 2A_mtl1_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 452R_low


title: 174R_high

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX ISW2-FRB-HIS3MX; Padh1-Os.TIR1


title: 452V_low


title: 174V_low


title: 174R_low


title: 521V_high

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 CHD1-FRB-KanMX; ISW1-aid*-9myc-HphNT Padh1-Os.TIR1:URA3


title: 521R_high


title: 521R_low


title: 254706910145_b3 - 3B_WT_before transfert_2 vs 1B_mtl1_before transfert_2

hyb_protocol: 1B_mtl1_before transfert_2 Cy5 / 3B_WT_before transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 521V_low


title: 174V_high


title: 254706910139_b4 - 6C_WT_rotenone-treated_12h after transfert_3 vs 5C_WT_untreated_12h after transfert_3

hyb_protocol: 5C_WT_untreated_12h after transfert_3 Cy5 / 6C_WT_rotenone-treated_12h after transfert_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 5C_WT_untreated_12h after transfert_3

growth_protocol: callus - Média: Arabidopsis liquid medium hygrometry: 70% Temperature: 21°C Light: 10h day / 12h night

tag: ecotype

value: Columbia

tag: harvest date

treatment_protocol: Name:Rotenone on callus - time course study - inhibition of mitochodrial etc,rotenone:. Inhibition of the the comlex I of the mitochodrial electron transport chain with rotenone


title: 254706910145_b2 - 1A_mtl1_before transfert_1 vs 3A_WT_before transfert_1

hyb_protocol: 3A_WT_before transfert_1 Cy5 / 1A_mtl1_before transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910145_b1 - 3A_WT_before transfert_1 vs 1A_mtl1_before transfert_1

hyb_protocol: 1A_mtl1_before transfert_1 Cy5 / 3A_WT_before transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910139_b3 - 5C_WT_untreated_12h after transfert_3 vs 6C_WT_rotenone-treated_12h after transfert_3

hyb_protocol: 6C_WT_rotenone-treated_12h after transfert_3 Cy5 / 5C_WT_untreated_12h after transfert_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910138_b4 - 6A_WT_rotenone-treated_12h after transfert_1 vs 5A_WT_untreated_12h after transfert_1

hyb_protocol: 5A_WT_untreated_12h after transfert_1 Cy5 / 6A_WT_rotenone-treated_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 5A_WT_untreated_12h after transfert_1


title: 458V_high

source_name: whole organism

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ISW2-FRB-HIS3MX; INO80-aid*-9myc-HphNT Padh1-Os.TIR1


title: 458R_high


title: 254706910138_b3 - 5A_WT_untreated_12h after transfert_1 vs 6A_WT_rotenone-treated_12h after transfert_1

hyb_protocol: 6A_WT_rotenone-treated_12h after transfert_1 Cy5 / 5A_WT_untreated_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 458R_low


title: 254706910138_b1 - 4C_WT_Rotenone7d_3 vs 6C_WT_rotenone-treated_12h after transfert_3

hyb_protocol: 6C_WT_rotenone-treated_12h after transfert_3 Cy5 / 4C_WT_Rotenone7d_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910139_b2 - 6B_WT_rotenone-treated_12h after transfert_2 vs 5B_WT_untreated_12h after transfert_2

hyb_protocol: 5B_WT_untreated_12h after transfert_2 Cy5 / 6B_WT_rotenone-treated_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 5B_WT_untreated_12h after transfert_2


title: 254706910145_b4 - 1B_mtl1_before transfert_2 vs 3B_WT_before transfert_2

hyb_protocol: 3B_WT_before transfert_2 Cy5 / 1B_mtl1_before transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 458V_low


title: 519R_high

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-HIS3MX SNF2-FRB-KanMX


title: 519V_high


title: 519R_low


title: 254706910137_b2 - 6A_WT_rotenone-treated_12h after transfert_1 vs 4A_WT_Rotenone7d_1

hyb_protocol: 4A_WT_Rotenone7d_1 Cy5 / 6A_WT_rotenone-treated_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910137_b4 - 6B_WT_rotenone-treated_12h after transfert_2 vs 4B_WT_Rotenone7d_2

hyb_protocol: 4B_WT_Rotenone7d_2 Cy5 / 6B_WT_rotenone-treated_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910137_b3 - 4B_WT_Rotenone7d_2 vs 6B_WT_rotenone-treated_12h after transfert_2

hyb_protocol: 6B_WT_rotenone-treated_12h after transfert_2 Cy5 / 4B_WT_Rotenone7d_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910138_b2 - 6C_WT_rotenone-treated_12h after transfert_3 vs 4C_WT_Rotenone7d_3

hyb_protocol: 4C_WT_Rotenone7d_3 Cy5 / 6C_WT_rotenone-treated_12h after transfert_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 519V_low

growth_protocol: cells were grown at 30 degrees in YPD to mid-log phase before treatment

extract_protocol:
Chromatin for MNase digestion was prepared essentially as described in Kubik et al., 2015 (GSE73337) (PMID: 26545077)
Libraries were prepared essentially as described in Henikoff et al., 2011 (GSE30551) (PMID: 22025700)


title: 254706910137_b1 - 4A_WT_Rotenone7d_1 vs 6A_WT_rotenone-treated_12h after transfert_1

hyb_protocol: 6A_WT_rotenone-treated_12h after transfert_1 Cy5 / 4A_WT_Rotenone7d_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910136_b2 - 5B_WT_untreated_12h after transfert_2 vs 3B_WT_untreated_2

hyb_protocol: 3B_WT_untreated_2 Cy5 / 5B_WT_untreated_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910136_b1 - 3B_WT_untreated_2 vs 5B_WT_untreated_12h after transfert_2

hyb_protocol: 5B_WT_untreated_12h after transfert_2 Cy5 / 3B_WT_untreated_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910136_b4 - 5C_WT_untreated_12h after transfert_3 vs 3C_WT_untreated_3

hyb_protocol: 3C_WT_untreated_3 Cy5 / 5C_WT_untreated_12h after transfert_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910135_b4 - 5A_WT_untreated_12h after transfert_1 vs 3A_WT_untreated_1

hyb_protocol: 3A_WT_untreated_1 Cy5 / 5A_WT_untreated_12h after transfert_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910136_b3 - 3C_WT_untreated_3 vs 5C_WT_untreated_12h after transfert_3

hyb_protocol: 5C_WT_untreated_12h after transfert_3 Cy5 / 3C_WT_untreated_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910135_b3 - 3A_WT_untreated_1 vs 5A_WT_untreated_12h after transfert_1

hyb_protocol: 5A_WT_untreated_12h after transfert_1 Cy5 / 3A_WT_untreated_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910139_b1 - 5B_WT_untreated_12h after transfert_2 vs 6B_WT_rotenone-treated_12h after transfert_2

hyb_protocol: 6B_WT_rotenone-treated_12h after transfert_2 Cy5 / 5B_WT_untreated_12h after transfert_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910135_b2 - 4C_WT_Rotenone7d_3 vs 2C_WT_Rotenone12h_3

hyb_protocol: 2C_WT_Rotenone12h_3 Cy5 / 4C_WT_Rotenone7d_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910134_b4 - 4B_WT_Rotenone7d_2 vs 2B_WT_Rotenone12h_2

hyb_protocol: 2B_WT_Rotenone12h_2 Cy5 / 4B_WT_Rotenone7d_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SV40_07

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: Twenty micrograms of total RNA from tissues were used to derive fluorescently (Cy5 or Cy3) labeled complementary DNA. A reference complementary DNA was generated using total RNA from 19 normal livers. At least two hybridizations were performed for each tissue sample using a dye-swap strategy to eliminate labeling bias of the fluorescent intensity measurement.

hyb_protocol: At least two hybridizations were carried out for each tissue using dye-swap strategy to eliminate dye labeling bias.

scan_protocol: Scanned with Axon GenePix 4000B, images and spot values acquired with GenePix Pro 5.1.0.19

data_processing: We transformed and normalized mouse gene expression and  averaged expression ratios of each gene from replicated experiments , selected genes with <30% missing expression data across the tissues in each data set and an expression ratio that differed from reference by a factor of at least 2 in at least 10% of tissues in each data set for further analysis

source_name: HCC tumor

label_protocol: To obtain gene expression profile data from four transgenic HCC mouse models, 20 μg of total RNAs from tissues were used to drive fluorescently (Cy-5 or Cy-3) labeled cDNA.

extract_protocol: Total RNAs were isolated from frozen liver tissue using CsCl density gradient centrifugation methods. Total RNA from the livers of 10 wild type mice were pooled and used as reference in entire microarray experiments.

value: simian vacuolating virus 40 (SV40) T-antigen transgenic model

value: liver


title: SV40_10


title: SV40_08


title: 254706910134_b1 - 2A_WT_Rotenone12h_1 vs 4A_WT_Rotenone7d_1

hyb_protocol: 4A_WT_Rotenone7d_1 Cy5 / 2A_WT_Rotenone12h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910134_b2 - 4A_WT_Rotenone7d_1 vs 2A_WT_Rotenone12h_1

hyb_protocol: 2A_WT_Rotenone12h_1 Cy5 / 4A_WT_Rotenone7d_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SV40_06


title: 254706910133_b4 - 4C_WT_Rotenone7d_3 vs 3C_WT_untreated_3

hyb_protocol: 3C_WT_untreated_3 Cy5 / 4C_WT_Rotenone7d_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SV40_05


title: SV40_03


title: 254706910134_b3 - 2B_WT_Rotenone12h_2 vs 4B_WT_Rotenone7d_2

hyb_protocol: 4B_WT_Rotenone7d_2 Cy5 / 2B_WT_Rotenone12h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SV40_04


title: SV40_01


title: 254706910132_b2 - 2C_WT_Rotenone12h_3 vs 1C_WT_untreated_3

hyb_protocol: 1C_WT_untreated_3 Cy5 / 2C_WT_Rotenone12h_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910131_b4 - 2B_WT_Rotenone12h_2 vs 1B_WT_untreated_2

hyb_protocol: 1B_WT_untreated_2 Cy5 / 2B_WT_Rotenone12h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.