title: PGK12.1_control RNAi-4

first: Joel

last: Berletch

address: 1959 NE Pacific St.

department: Pathology

institute: University of Washington

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after 48h treatment of 100pmol of negative control siRNAs (Invitrogen Stealth control). Kdm6a single-RNAi experiment 4 in PGK12.1.

hyb_protocol: Hybridization and washing were performed according to the standard Affymetrix protocol.

scan_protocol: Array hybridizations were done at the Microarray Facility at CHDD (University of Washington, Seattle WA).

data_processing: Raw data files from paired RNAi experiments were analyzed with Affymetrix® Expression Console™ Software using the RMA gene default.

source_name: Mouse female ES cells PGK12.1 after single RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-4 in PGK12.1.

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

growth_protocol: ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for RNAi experiments and cell collection.

extract_protocol: Total RNA was prepared by the Qiagen RNeasy kit with on-column DNaseI digestion

treatment_protocol: 100pmol of gene-specific siRNAs or negative control siRNAs (Invitrogen Stealth) were transfected into 2x105 ES or MEF cells in six-well plates using a standard reverse transfection protocol with Lipofectamine RNAiMax (Invitrogen).  Cells were harvested after 48h of RNAi treatment. For the double RNAi knockdown of Kdm6a, after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest.

tag: background strain

value: Derived from blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

value: ES cell

tag: passage


title: WD44_Kdm6a RNAi-1

status: Public on Mar 13 2013

type: RNA

city: Seattle

state: WA

country: USA

description: Gene expression data from mouse undifferentiated male ES cells WD44 after 48h treatment of 100pmol of Kdm6a siRNAs. Kdm6a single-RNAi experiment 1 in WD44.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse male ES cells WD44 after single RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-1 in WD44.

value: Derived from BL6 blastcysts.

tag: cell line

tag: cell type


title: PGK12.1_Kdm6a RNAi-3

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after 48h treatment of 100pmol of Kdm6a siRNAs. Kdm6a single-RNAi experiment 3 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after single RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-3 in PGK12.1.


title: H3 antibody3 OR Head Nuclear D.melanogaster ChIP Rep1

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: H3 antibody3 OR Head Nuc. ChIP expt.1811 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Collection of fly heads from whole adults using sieves of varying sizes.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: strain

value: Oregon-R

tag: developmental stage

value: Mixed Adult

tag: genotype

value: wild type


title: WD44_Kdm6a RNAi-2

description: Gene expression data from mouse undifferentiated male ES cells WD44 after 48h treatment of 100pmol of Kdm6a siRNAs. Kdm6a single-RNAi experiment 2 in WD44.

source_name: Mouse male ES cells WD44 after single RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-2 in WD44.


title: WD44_control RNAi-1

description: Gene expression data from mouse undifferentiated male ES cells WD44 after 48h treatment of 100pmol of negative control siRNAs (Invitrogen Stealth control). Kdm6a single-RNAi experiment 1 in WD44.

source_name: Mouse male ES cells WD44 after single RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-1 in WD44.


title: PGK12.1_control RNAi-2

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs (Invitrogen Stealth control), in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. Kdm6a double-RNAi experiment-2 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-2 in PGK12.1.


title: H3 antibody3 OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1812.Mvalues.bedgraph

source_name: H3 antibody3 OR Head Nuc. Input expt.1790 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.


title: H3 antibody3 OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1811.Mvalues.bedgraph

source_name: H3 antibody3 OR Head Nuc. Input expt.1789 channel_1


title: WD44_control RNAi-2

description: Gene expression data from mouse undifferentiated male ES cells WD44 after 48h treatment of 100pmol of negative control siRNAs (Invitrogen Stealth control). Kdm6a single-RNAi experiment 2 in WD44.

source_name: Mouse male ES cells WD44 after single RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-2 in WD44.


title: PGK12.1_control RNAi-3

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after 48h treatment of 100pmol of negative control siRNAs (Invitrogen Stealth control). Kdm6a single-RNAi experiment 3 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after single RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-3 in PGK12.1.


title: PGK12.1_Kdm6a RNAi-4

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after 48h treatment of 100pmol of Kdm6a siRNAs. Kdm6a single-RNAi experiment 4 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after single RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-4 in PGK12.1.


title: PGK12.1_Kdm6a RNAi-2

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of Kdm6a siRNAs, in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. Kdm6a double-RNAi experiment-2 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after double RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-2 in PGK12.1.


title: PGK12.1_Kdm6a RNAi-1

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of Kdm6a siRNAs, in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. Kdm6a double-RNAi experiment-1 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after double RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-1 in PGK12.1.


title: H3 antibody3 L3 Nuclear D.melanogaster ChIP Rep2

source_name: H3 antibody3 L3 Nuc. ChIP expt.953 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: 3rd Instar Larvae


title: wildtype, stress, biological rep5

city: Muenster

first: Christa

last: Hohoff

address: Albert-Schweitzer-Campus 1, A9

department: Psychiatry

country: Germany

institute: University of Muenster

description: Gene expression data from amygdalae of wildtype mouse after stress

hyb_protocol: Hybridisation of the cartridge arrays was performed following the GeneChip WT Sense Target label User Manual for use with Affymetrix GeneChip Hybridization Wash and Stain Kit.

scan_protocol: Arrays were scanned with an Affymetrix GCS3000 7G using the AGCC Scan Control 1.1.0.845.

data_processing: The data were analyzed with ArrayAssist Software (Stratagene/Agilent), using ExonRMA algorithm. This includes quantile normalization, PM-GCBG background correction, variance stabilization and transformation of the data on logarithmic scale.

label_protocol: The samples were processed using the WT cDNA Synthesis and Amplification Kit for Affymetrix GeneChip Whole Transcript (WT) Expression Arrays. Labeling was performed following the GeneChip WT Sense Target Labeling Assay User Manual (100 ng Total RNA Labeling Protocol) for use with Affymetrix WT Sense Target Labeling and Control Reagents.

growth_protocol: Test animals were descendants from heterozygous (+/-) 5-HTT knockout mice generated on C57BL/6 background (Bengel, Murphy et al. 1998). They were weaned at 21 days of age to be maintained in sibling groups and transferred to single housing at 5 months of age two months prior to treatment.

extract_protocol: Tissue was homogenized in 2X Nucleic Acid Purification Lysis Solution (Applied Biosystems, Life Technologies); total RNA was extracted using ABI 6100 Nucleic Acid PrepStation with Total RNA Chemistry following the manufacturer’s instructions (Applied Biosystems) including preceding Proteinase K digestion (0.4 mg/sample at RT).

treatment_protocol: Elevated pus-maze (EPM) test was performed at seven months of age. Two weeks later each mouse was subjected to either control condition (1 min. homecage) or acute stress condition (1 min. in cold water, 22°C) followed by anaesthesia (isoflurane) and decapitation for blood collection and amygdalae dissection for RNA extraction.

tag: genetic background

value: wildtype, descendant from heterozygous parents

tag: gender

value: male

tag: age

value: seven months

tag: tissue

value: amygdalae (left+right)

tag: treatment

value: acute stressor (1 min. in cold water, 22°C)


title: H3 antibody3 L3 Nuclear D.melanogaster Input Rep2

description: Served as Input for: 953.Mvalues.bedgraph

source_name: H3 antibody3 L3 Nuc. Input expt.903 channel_1


title: H3 antibody3 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3 antibody3 2-4 hr OR Em. ChIP expt.951 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Embryo 2-4hr OR


title: H3 antibody3 L3 Nuclear D.melanogaster Input Rep1

description: Served as Input for: 952.Mvalues.bedgraph

source_name: H3 antibody3 L3 Nuc. Input expt.902 channel_1


title: PGK12.1_control RNAi-1

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs (Invitrogen Stealth control), in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. Kdm6a double-RNAi experiment-1 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-1 in PGK12.1.


title: wildtype, control, biological rep4

description: Gene expression data from amygdalae of control wildtype mouse

source_name: amygdalae of control wildtype mouse

value: control condition (1 min. homecage)


title: H3 antibody3 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3 antibody3 2-4 hr OR Em. ChIP expt.950 channel_1


title: knockout, stress, biological rep5

description: Gene expression data from amygdalae of 5-HTT knockout mouse after stress

value: 5-HTT knockout, descendant from heterozygous parents


title: knockout, stress, biological rep4

source_name: amygdalae of 5-HTT knockout mouse after stress


title: wildtype, stress, biological rep4

source_name: amygdalae of wildtype mouse after stress


title: wildtype, control, biological rep5


title: H3 antibody3 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 950.Mvalues.bedgraph

source_name: H3 antibody3 2-4 hr OR Em. Input expt.1001 channel_1


title: H3 antibody3 L3 Nuclear D.melanogaster ChIP Rep1

source_name: H3 antibody3 L3 Nuc. ChIP expt.952 channel_1


title: H3 antibody3 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 951.Mvalues.bedgraph

source_name: H3 antibody3 2-4 hr OR Em. Input expt.1002 channel_1


title: Smc3 Q2580 S2-DRSC D.melanogaster ChIP Rep1

source_name: Smc3 Q2580 S2 ChIP expt.1027 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: embryo-derived cell-line

value: late embryonic stage

tag: Sex

value: Male


title: Smc3 Q2580 S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 1203.Mvalues.bedgraph

source_name: Smc3 Q2580 S2 Input expt.1191 channel_1


title: knockout, control, biological rep4

description: Gene expression data from amygdalae of control 5-HTT knockout mouse


title: wildtype, control, biological rep3


title: knockout, stress, biological rep3


title: knockout, control, biological rep3

source_name: amygdalae of control 5-HTT knockout mouse


title: knockout, control, biological rep5


title: Smc3 Q2580 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 1027.Mvalues.bedgraph

source_name: Smc3 Q2580 S2 Input expt.767 channel_1


title: knockout, stress, biological rep2


title: knockout, stress, biological rep1


title: Smc3 Q2580 S2-DRSC D.melanogaster ChIP Rep2

source_name: Smc3 Q2580 S2 ChIP expt.1203 channel_1


title: knockout, control, biological rep1


title: wildtype, control, biological rep2


title: knockout, control, biological rep2


title: wildtype, stress, biological rep3


title: wildtype, stress, biological rep2


title: wildtype, control, biological rep1


title: Hypoxia_100_Brain_11

city: Oslo

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

country: Norway

institute: University of Oslo

hyb_protocol: GeneChip Hybridization Oven, 16-18 hours, 45oC, 60 rotations/min; washing and staining on Fluidics Station 450, protocol FS450_0007

scan_protocol: GeneChip Scanner 3000 7G controlled by GeneChip Operating Software

data_processing: Robust multiarray average (R/Bioconductor, using the library aroma.affymetrix)

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep11

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Ficoll isopaque gradient centrifugation and RiboPure Blood Kit (Ambion, Life Technologies, Carlsbad, USA) were used for total RNA extraction

value: Brain

value: Postnatal day seven

tag: hypoxia or normoxia group

value: Hypoxia

tag: reoxygenated with


title: wildtype, stress, biological rep1


title: Hypoxia_60_Eye_9

source_name: Hypoxia group_reoxygenated with 60 % O2_Eye_rep_9

value: Eye


title: Hypoxia_100_Eye_11

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_11


title: Hypoxia_60_Eye_8

source_name: Hypoxia group_reoxygenated with 60 % O2_Eye_rep_8


title: Hypoxia_100_Eye_10

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_10


title: Hypoxia_60_Brain_11

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep11


title: Hypoxia_100_Brain_10

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep10


title: Hypoxia_40_Eye_10

source_name: Hypoxia group_reoxygenated with 40 % O2_Eye_rep_10


title: Hypoxia_40_Eye_8

source_name: Hypoxia group_reoxygenated with 40 % O2_Eye_rep_8


title: KMS12 shCasp10-2 - day 2 - mAdbID:91461

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 91461

hyb_protocol: Sample Hybridization Protocol Other: For hybridization to the array, the Cy3 reaction was added to the Cy5 reaction for each array and placed onto a Microcom YM30 column (Amicon). The column was centrifuged at 14K for approximately 7 minutes, so that 20-40 microliters of probe remained. Flow-through from column was discarded, and an additional 400 microliters TE was applied to the column. Also added to the column was: 20 microliters cot-1 DNA (10 µg/µl, Roche), 2 microliters yeast tRNA (2µg/µl, Sigma), 2 microliters poly d(A) (8µg/µl, Amersham). The column was centrifuged for approximately 7 minutes until there was approximately 20 microliters left. The column was inverted into a fresh tube and centrifuged for 30 seconds to elute probe. TE was added to bring up volume to 25 µl. SDS (0.75 µl of 10% SDS) 20x SSC (4.25 µl) were added to the sample. The sample was incubated at 100oC for 2 minutes and then centrifuged for 30 sec at 13,000 RPM. The probe (30 µl) was applied to the microarray and covered with a coverslip (Fisher #02-671-35), being careful to avoid bubbles. Water (40 µl) was added in small droplets to each side of the slide to maintain humidity after which the hybridization chamber was closed and and place at 65oC overnight. The hybridized slide was washed as follows: 2xSSC + 0.1% SDS for 1 min, 1xSSC for 1 min x 2 washess, 0.5xSSC for 1 min, 0.2xSSC for 1 min. The slide was centrifuged immediately in slide holder in swinging bucket rotor at 550 rpm for 5 min, and then scanned.

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 710;; 660 ScanPower: 100;; 100 LaserPower: 3.15;; 2.66 Temperature: 31.24

data_processing:
Data Processing Protocol
Calculation Method: Background correction was done using mean intensity minus median background. Calculations were based on signals greater than 100 in both channels and excluding features designated as controls or flagged as bad or not found. Ratios were normalized using the 50th percentile (median).

organism: Homo sapiens

source_name: KMS12 shCasp10-2 with DOX - day 2

label_protocol:
Cy5 Labeling Protocol
Other: 50 ug of total RNA was labeled with Cy5.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 48 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2. shRNA expression was induced with doxycycline for 48 hours.

value: shCasp10-2 with DOX

tag: time

value: day 2

value: blood

value: multiple myeloma

tag: disease state

source_name: KMS12 shCasp10-2 uninduced - day 2

label_protocol:
Cy3 Labeling Protocol
Other: 50 ug of total RNA was labeled with Cy3.

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2.

value: shCasp10-2 uninduced


title: Hypoxia_40_Eye_9

source_name: Hypoxia group_reoxygenated with 40 % O2_Eye_rep_9


title: Hypoxia_60_Brain_10

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep10


title: KMS12 shCasp10-2 - day 1 - mAdbID:91460

description: mAdb experiment ID: 91460

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 690;; 640 ScanPower: 100;; 100 LaserPower: 3.25;; 2.63 Temperature: 31.03

source_name: KMS12 shCasp10-2 with DOX - day 1

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 24 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2. shRNA expression was induced with doxycycline for 24 hours.

value: day 1

source_name: KMS12 shCasp10-2 uninduced - day 1

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2.


title: KMS12 shCasp10-2 - day 4 - mAdbID:91463

description: mAdb experiment ID: 91463

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 710;; 660 ScanPower: 100;; 100 LaserPower: 3.09;; 2.71 Temperature: 31.48

source_name: KMS12 shCasp10-2 with DOX - day 4

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 96 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2. shRNA expression was induced with doxycycline for 96 hours.

value: day 4

source_name: KMS12 shCasp10-2 uninduced - day 4

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2.


title: H929 shCasp10-2 - day 2 - repeat 1 - mAdbID:91457

description: mAdb experiment ID: 91457

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 680;; 620 ScanPower: 100;; 100 LaserPower: 3.22;; 2.47 Temperature: 30.54

source_name: H929 shCasp10-2 with DOX - day 2

source_name: H929 shCasp10-2 uninduced - day 2


title: H929 shCasp10-2 - day 3 - repeat 1 - mAdbID:91458

description: mAdb experiment ID: 91458

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 690;; 630 ScanPower: 100;; 100 LaserPower: 3.3;; 2.72 Temperature: 30.69

source_name: H929 shCasp10-2 with DOX - day 3

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 72 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2. shRNA expression was induced with doxycycline for 72 hours.

value: day 3

source_name: H929 shCasp10-2 uninduced - day 3

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2.


title: KMS12 shCasp10-2 - day 3 - mAdbID:91462

description: mAdb experiment ID: 91462

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 710;; 660 ScanPower: 100;; 100 LaserPower: 3.17;; 2.72 Temperature: 31.36

source_name: KMS12 shCasp10-2 with DOX - day 3

source_name: KMS12 shCasp10-2 uninduced - day 3


title: SKMM1 shCasp10-2 and shCtrl - day 4 - mAdbID:91214

description: mAdb experiment ID: 91214

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 850;; 590 ScanPower: 100;; 100 LaserPower: 2.92;; 3.31 Temperature: 31.97

source_name: SKMM1 shCasp10-2 with DOX - day 4

source_name: SKMM1 shCtrl with DOX - day 4

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 96 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing a control shRNA. shRNA expression was induced with doxycycline for 96 hours.

value: shCtrl with DOX


title: SKMM1 shCasp10-2 and shCtrl - day 3 - mAdbID:91213

description: mAdb experiment ID: 91213

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 870;; 560 ScanPower: 100;; 100 LaserPower: 2.89;; 3.33 Temperature: 31.85

source_name: SKMM1 shCasp10-2 with DOX - day 3

source_name: SKMM1 shCtrl with DOX - day 3

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 72 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing a control shRNA. shRNA expression was induced with doxycycline for 72 hours.


title: SKMM1 shCasp10-2 and shCtrl - day 2 - mAdbID:91212

description: mAdb experiment ID: 91212

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 870;; 580 ScanPower: 100;; 100 LaserPower: 2.88;; 3.27 Temperature: 31.76

source_name: SKMM1 shCasp10-2 with DOX - day 2

source_name: SKMM1 shCtrl with DOX - day 2

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 48 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing a control shRNA. shRNA expression was induced with doxycycline for 48 hours.


title: Hypoxia_40_Brain_10

source_name: Hypoxia group_reoxygenated with 40 % O2_Brain_rep10


title: H929 shCasp10-2 - day 4 - repeat 1 - mAdbID:91459

description: mAdb experiment ID: 91459

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 690;; 630 ScanPower: 100;; 100 LaserPower: 3.29;; 2.62 Temperature: 30.87

source_name: H929 shCasp10-2 with DOX - day 4

source_name: H929 shCasp10-2 uninduced - day 4


title: H929 shCasp10-2 - day 1 - mAdbID:91456

description: mAdb experiment ID: 91456

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 680;; 620 ScanPower: 100;; 100 LaserPower: 3.23;; 3.27 Temperature: 30.36

source_name: H929 shCasp10-2 with DOX - day 1

source_name: H929 shCasp10-2 uninduced - day 1


title: Control_21_Eye_8

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Eye_rep_8

value: Normoxia (control)


title: SKMM1 shCasp10-2 - day 1 - mAdbID:91210

description: mAdb experiment ID: 91210

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 780;; 600 ScanPower: 100;; 100 LaserPower: 3.1;; 3.49 Temperature: 30.57

source_name: SKMM1 shCasp10-2 with DOX - day 1

source_name: SKMM1 shCasp10-2 uninduced - day 1


title: Control_21_Eye_7

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Eye_rep_7


title: Hypoxia_40_Brain_9

source_name: Hypoxia group_reoxygenated with 40 % O2_Brain_rep9


title: SKMM1 shCasp10-2 and shCtrl - day 1 - mAdbID:91211

description: mAdb experiment ID: 91211

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 850;; 600 ScanPower: 100;; 100 LaserPower: 2.9;; 3.39 Temperature: 31.58

source_name: SKMM1 shCtrl with DOX - day 1

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 24 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing a control shRNA. shRNA expression was induced with doxycycline for 24 hours.


title: Hypoxia_100_Brain_9

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep9


title: Control_21_Eye_9

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Eye_rep_9


title: Hypoxia_21_Brain_9

source_name: Hypoxia group_reoxygenated with 21 % O2_Brain_rep9


title: Control_21_Brain_7

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Brain_rep7


title: Control_21_Brain_9

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Brain_rep9


title: SKMM1 shCasp10-2 - day 4 - repeat 1 - mAdbID:91207

description: mAdb experiment ID: 91207

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 840;; 600 ScanPower: 100;; 100 LaserPower: 2.99;; 2.81 Temperature: 31.36

source_name: SKMM1 shCasp10-2 with DOX - day 4

source_name: SKMM1 shCasp10-2 uninduced - day 4


title: Control_21_Brain_8

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Brain_rep8


title: SKMM1 shCasp10-2 - day 3 - repeat 1 - mAdbID:91208

description: mAdb experiment ID: 91208

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 840;; 600 ScanPower: 100;; 100 LaserPower: 3;; 3.19 Temperature: 31.18

source_name: SKMM1 shCasp10-2 with DOX - day 3

source_name: SKMM1 shCasp10-2 uninduced - day 3


title: Hypoxia_21_Eye_9

source_name: Hypoxia group_reoxygenated with 21 % O2_Eye_rep_9


title: Hypoxia_40_Brain_8

source_name: Hypoxia group_reoxygenated with 40 % O2_Brain_rep8


title: H929 shCasp10-3 - day 3 - mAdbID:88061

description: mAdb experiment ID: 88061

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 680;; 590 ScanPower: 100;; 100 LaserPower: 2.93;; 2.89 Temperature: 33.16

source_name: H929 shCasp10-3 with DOX - day 3

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 72 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-3. shRNA expression was induced with doxycycline for 72 hours.

value: shCasp10-3 with DOX

source_name: H929 shCasp10-3 uninduced - day 3

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-3.

value: shCasp10-3 uninduced


title: Hypoxia_100_Eye_9

scan_protocol: GeneChip Scanner 3000 7G controlled by GeneChip Operating Software

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_9


title: Hypoxia_100_Eye_8

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_8


title: H929 shCasp10-3 - day 4 - mAdbID:88062

description: mAdb experiment ID: 88062

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 670;; 590 ScanPower: 100;; 100 LaserPower: 2.96;; 3.32 Temperature: 33.41

source_name: H929 shCasp10-3 with DOX - day 4

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 96 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-3. shRNA expression was induced with doxycycline for 96 hours.

source_name: H929 shCasp10-3 uninduced - day 4

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-3.


title: Hypoxia_21_Brain_8

source_name: Hypoxia group_reoxygenated with 21 % O2_Brain_rep8


title: KMS12 shCasp10-3 - day 4 - mAdbID:87893

description: mAdb experiment ID: 87893

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 760;; 610 ScanPower: 100;; 100 LaserPower: 3.08;; 3.48 Temperature: 32.52

source_name: KMS12 shCasp10-3 with DOX - day 4

source_name: KMS12 shCasp10-3 uninduced - day 4


title: Hypoxia_100_Brain_8

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep8


title: KMS12 shCasp10-3 - day 5 - mAdbID:87894

description: mAdb experiment ID: 87894

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 740;; 610 ScanPower: 100;; 100 LaserPower: 3.06;; 3.48 Temperature: 32.64

source_name: KMS12 shCasp10-3 with DOX - day 5

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 120 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-3. shRNA expression was induced with doxycycline for 120 hours.

value: day 5

source_name: KMS12 shCasp10-3 uninduced - day 5

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 120 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-3.


title: SKMM1 shCasp10-2 - day 2 - repeat 1 - mAdbID:91209

description: mAdb experiment ID: 91209

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 850;; 600 ScanPower: 100;; 100 LaserPower: 3.08;; 3.41 Temperature: 30.87

source_name: SKMM1 shCasp10-2 with DOX - day 2

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 48 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2. shRNA expression was induced with doxycycline for 48 hours.

source_name: SKMM1 shCasp10-2 uninduced - day 2

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2.


title: H929 shCasp10-3 - day 5 - mAdbID:88063

description: mAdb experiment ID: 88063

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 710;; 580 ScanPower: 100;; 100 LaserPower: 3;; 3.36 Temperature: 33.47

source_name: H929 shCasp10-3 with DOX - day 5

source_name: H929 shCasp10-3 uninduced - day 5


title: KMS12 shCasp10-3 - day 2 - mAdbID:87891

description: mAdb experiment ID: 87891

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 720;; 610 ScanPower: 100;; 100 LaserPower: 3.06;; 3.26 Temperature: 31.73

source_name: KMS12 shCasp10-3 with DOX - day 2

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 48 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-3. shRNA expression was induced with doxycycline for 48 hours.

source_name: KMS12 shCasp10-3 uninduced - day 2

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-3.


title: H929 shCasp10-3 - day 2 - mAdbID:88060

description: mAdb experiment ID: 88060

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 720;; 610 ScanPower: 100;; 100 LaserPower: 2.97;; 2.9 Temperature: 32.98

source_name: H929 shCasp10-3 with DOX - day 2

source_name: H929 shCasp10-3 uninduced - day 2


title: KMS12 shCasp10-3 - day 3 - mAdbID:87892

description: mAdb experiment ID: 87892

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 710;; 580 ScanPower: 100;; 100 LaserPower: 3.12;; 3.01 Temperature: 32.22

source_name: KMS12 shCasp10-3 with DOX - day 3

source_name: KMS12 shCasp10-3 uninduced - day 3


title: SKMM1 shCasp10-2 - day 4 - repeat 2 - mAdbID:87402

description: mAdb experiment ID: 87402

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 770;; 620 ScanPower: 100;; 100 LaserPower: 3.08;; 3.41 Temperature: 31.12

source_name: SKMM1 shCasp10-2 with DOX - day 4

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 96 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2. shRNA expression was induced with doxycycline for 96 hours.

source_name: SKMM1 shCasp10-2 uninduced - day 4

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2.


title: SKMM1 shCasp10-2 - day 5 - repeat 1 - mAdbID:87401

description: mAdb experiment ID: 87401

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 680;; 600 ScanPower: 100;; 100 LaserPower: 3.11;; 3.44 Temperature: 30.9

source_name: SKMM1 shCasp10-2 with DOX - day 5

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 120 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2. shRNA expression was induced with doxycycline for 120 hours.

source_name: SKMM1 shCasp10-2 uninduced - day 5

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 120 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2.


title: Control_21_Lung_9

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Lung_rep_9

value: Lung


title: Hypoxia_40_Lung_9

source_name: Hypoxia group_reoxygenated with 40 % O2_Lung_rep_9

value: Postnatal day seven


title: Hypoxia_40_Lung_10

source_name: Hypoxia group_reoxygenated with 40 % O2_Lung_rep_10

value: Hypoxia


title: Hypoxia_100_Lung_11

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_11


title: SKMM1 shCasp10-2 - day 3 - repeat 2 - mAdbID:87404

description: mAdb experiment ID: 87404

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 730;; 620 ScanPower: 100;; 100 LaserPower: 3.04;; 3.34 Temperature: 31.3

source_name: SKMM1 shCasp10-2 with DOX - day 3

treatment_protocol:
Treatment type: shRNA transduction
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 72 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2. shRNA expression was induced with doxycycline for 72 hours.

source_name: SKMM1 shCasp10-2 uninduced - day 3

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hours
In-vivo treatment: Cell line was transduced with retroviral vectors expressing shCasp10-2.


title: Hypoxia_21_Lung_9

source_name: Hypoxia group_reoxygenated with 21 % O2_Lung_rep_9


title: Control_100_Lung_10

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Lung_rep_10


title: Hypoxia_60_Lung_11

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_11


title: Hypoxia_60_Brain_9

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep9

value: Brain


title: OCI-Ly19 shCasp10-2 - day 4 - mAdbID:87398

description: mAdb experiment ID: 87398

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 740;; 610 ScanPower: 100;; 100 LaserPower: 2.92;; 3.51 Temperature: 31.58

source_name: OCI-Ly19 shCasp10-2 with DOX - day 4

value: shCasp10-2 with DOX

value: Diffuse Large B-cell Lymophoma (DLBCL)

value: Diffuse large B cell lymphoma (DLBCL)

source_name: OCI-Ly19 shCasp10-2 uninduced - day 4


title: SKMM1 shCasp10-2 - day 2 - repeat 2 - mAdbID:87399

description: mAdb experiment ID: 87399

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 740;; 610 ScanPower: 100;; 100 LaserPower: 2.96;; 3.5 Temperature: 31.48

source_name: SKMM1 shCasp10-2 with DOX - day 2

value: day 2

value: blood

value: multiple myeloma

source_name: SKMM1 shCasp10-2 uninduced - day 2


title: Hypoxia_100_Lung_10

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_10


title: H929 shCasp10-2 - day 4 - repeat 2 - mAdbID:81742

description: mAdb experiment ID: 81742

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 770;; 680 ScanPower: 100;; 100 LaserPower: 3.26;; 2.45 Temperature: 29.84

source_name: H929 shCasp10-2 with DOX - day 4

value: day 4

source_name: H929 shCasp10-2 uninduced - day 4

value: shCasp10-2 uninduced


title: H929 shCasp10-2 - day 3 - repeat 2 - mAdbID:81625

description: mAdb experiment ID: 81625

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 670 ScanPower: 100;; 100 LaserPower: 3.08;; 2.75 Temperature: 30.23

source_name: H929 shCasp10-2 with DOX - day 3

value: day 3

source_name: H929 shCasp10-2 uninduced - day 3


title: Control_21_Lung_8

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Lung_rep_8

value: Normoxia (control)


title: OCI-Ly7 shCasp10-2 - day 3 - mAdbID:81164

description: mAdb experiment ID: 81164

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 690 ScanPower: 100;; 100 LaserPower: 3.04;; 3.48 Temperature: 31.48

source_name: OCI-Ly7 shCasp10-2 with DOX - day 3

source_name: OCI-Ly7 shCasp10-2 uninduced - day 3


title: SKMM1 shCasp10-2 - day 5 - repeat 2 - mAdbID:81163

description: mAdb experiment ID: 81163

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 750;; 650 ScanPower: 100;; 100 LaserPower: 3.08;; 3.48 Temperature: 31.33

source_name: SKMM1 shCasp10-2 with DOX - day 5

source_name: SKMM1 shCasp10-2 uninduced - day 5


title: H929 shCasp10-2 - day 5 - mAdbID:81743

description: mAdb experiment ID: 81743

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 810;; 700 ScanPower: 100;; 100 LaserPower: 3.08267;; 2.5605 Temperature: 30.1416

source_name: H929 shCasp10-2 with DOX - day 5

source_name: H929 shCasp10-2 uninduced - day 5


title: OCI-Ly7 shCasp10-2 - day 4 - mAdbID:81166

description: mAdb experiment ID: 81166

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 690 ScanPower: 100;; 100 LaserPower: 3.04;; 2.62 Temperature: 31.61

source_name: OCI-Ly7 shCasp10-2 with DOX - day 4

source_name: OCI-Ly7 shCasp10-2 uninduced - day 4


title: OCI-Ly19 shCasp10-2 - day 3 - mAdbID:87397

description: mAdb experiment ID: 87397

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 590 ScanPower: 100;; 100 LaserPower: 3.04;; 3.16 Temperature: 30.54

source_name: OCI-Ly19 shCasp10-2 with DOX - day 3

source_name: OCI-Ly19 shCasp10-2 uninduced - day 3


title: SKMM1 shCasp10-2 - day 2 - repeat 3 - mAdbID:81162

description: mAdb experiment ID: 81162

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 760;; 650 ScanPower: 100;; 100 LaserPower: 3.13;; 3.2 Temperature: 30.87

source_name: SKMM1 shCasp10-2 with DOX - day 2

source_name: SKMM1 shCasp10-2 uninduced - day 2


title: Hypoxia_100_Lung_9

scan_protocol: GeneChip Scanner 3000 7G controlled by GeneChip Operating Software

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_9


title: SKMM1 shCasp10-2 - day 3 - repeat 3 - mAdbID:81161

description: mAdb experiment ID: 81161

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 780;; 610 ScanPower: 100;; 100 LaserPower: 3.14;; 3.47 Temperature: 31

source_name: SKMM1 shCasp10-2 with DOX - day 3

source_name: SKMM1 shCasp10-2 uninduced - day 3


title: Free floating DDC neurosphere NNI-1 replicate 2

city: Cambridge

first: Felicia

last: Ng

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

country: United Kingdom

institute: Cambridge Institute for Medical Research

description:
replicate 2
4672031023_D

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed using variance stabilizing transformation (VST) and quantile normalized.  Probes with detection p-val ≥ 0.01 and non-exonic probes were removed.

source_name: Primary neurosphere

label_protocol: Standard Illumina label protocol

growth_protocol: Graded brain tumor specimens were obtained with informed consent, as part of a study protocol approved by the institutional review board. Cells were seeded at a density of 2,500 per cm2 in chemically defined serum-free selection growth medium consisting of basic fibroblast growth factor, bFGF (20ng/ml, Chemicon), epidermal growth factor, EGF (20ng/ml, Chemicon), heparin (5µg/ml, Sigma-Aldrich) and serm-free supplement, B27 (1x, Gibco) in a 3:1 mix of Dulbecco’s Modified Eagle Medium (Sigma-Aldrich) and F-12 Nutrient Mixture (Gibco).  The cultures were incubated at 37 deg C in a water-saturated atmosphere containing 5% CO2 and 95% air.  To maintain the undifferentiated state of neurosphere cultures, growth factors were replenished every 2 days.  Successful neurosphere cultures (1 to 4 weeks) were expanded by mechanical trituration using a flame-drawn glass Pasteur pipette, and cells were re-seeded at 100,000 per ml in fresh medium. CD133(+) and CD133(-) cells were obtained after staining with anti-CD133 antibody conjugated to allophycocyanin (Clone 293C, Miltenyi Biotec) according to the manufacturer's protocol, and then flow-sorted on a BD FACSAria. Dead cells were excluded with a viability dye, 7-AAD (BD Pharmingen). Diphenylene iodonium (DPI)-treated cells were obtained after treatment with 5mM DPI (Sigma-Aldrich) for 1 hour. Diethyldithiocarbamate (DDC)-treated cells were obtained after treatment with 10mM DDC (Sigma-Aldrich) for 1 hour.

extract_protocol: Total RNA was isolated from neurosphere cells using TRI Reagent (Molecular Research Center) and purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). Reverse transcription and cRNA amplification were performed using an RNA Amplification kit (Ambion, Austin, TX).

tag: histology

value: Glioblastoma multiforme

tag: growth pattern

value: Free floating

value: DDC

tag: individual

value: Primary neurosphere


title: Hypoxia_40_Lung_8

source_name: Hypoxia group_reoxygenated with 40 % O2_Lung_rep_8

value: Lung

value: Postnatal day seven


title: Semi-adherent DPI neurosphere NNI-4 replicate 3

description:
replicate 3
4672031022_G

value: Semi-adherent

value: DPI


title: Semi-adherent DDC neurosphere NNI-4 replicate 2

description:
replicate 2
4672031023_G


title: Hypoxia_21_Lung_8

source_name: Hypoxia group_reoxygenated with 21 % O2_Lung_rep_8

value: Hypoxia


title: Control_100_Lung_9

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Lung_rep_9


title: SKMM1 shCasp10-2 - day 4 - repeat 3 - mAdbID:81160

description: mAdb experiment ID: 81160

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 700;; 640 ScanPower: 100;; 100 LaserPower: 3.12;; 3.47 Temperature: 31.06

source_name: SKMM1 shCasp10-2 with DOX - day 4

value: shCasp10-2 with DOX

tag: cell line

tag: cell type

source_name: SKMM1 shCasp10-2 uninduced - day 4


title: Hypoxia_100_Lung_8

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_8

tag: strain


title: Hypoxia_100_Lung_7

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_7


title: Hypoxia_21_Lung_7

source_name: Hypoxia group_reoxygenated with 21 % O2_Lung_rep_7


title: Control_21_Lung_6

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Lung_rep_6


title: Free floating DPI neurosphere NNI-1 replicate 3

description:
replicate 3
4672031022_D


title: Hypoxia_60_Lung_9

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_9


title: Hypoxia_40_Lung_7

source_name: Hypoxia group_reoxygenated with 40 % O2_Lung_rep_7


title: Semi-adherent DDC neurosphere NNI-4 replicate 4

description:
replicate 4
4672031022_H


title: Free floating DDC neurosphere NNI-8 replicate 4

description:
replicate 4
4672031018_F

value: Anaplastic oligoastrocytoma


title: H929 shCasp10-2 - day 2 - repeat 2 - mAdbID:81624

description: mAdb experiment ID: 81624

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 680 ScanPower: 100;; 100 LaserPower: 3.11;; 3.12 Temperature: 29.99

source_name: H929 shCasp10-2 with DOX - day 2

value: day 2

value: blood

source_name: H929 shCasp10-2 uninduced - day 2


title: Control_21_Lung_7

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Lung_rep_7


title: Free floating DPI neurosphere NNI-1 replicate 1

description:
replicate 1
4672031023_C


title: Semi-adherent DPI neurosphere NNI-4 replicate 1

description:
replicate 1
4672031023_F


title: Free floating DDC neurosphere NNI-8 replicate 2

description:
replicate 2
4672031018_B


title: Free floating DPI neurosphere NNI-8 replicate 3

description:
replicate 3
4672031018_E


title: Free floating DPI neurosphere NNI-8 replicate 1

description:
replicate 1
4672031018_A


title: Hypoxia_60_Lung_8

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_8


title: Hypoxia_60_Lung_12

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_12


title: Hypoxia_21_Eye_8

source_name: Hypoxia group_reoxygenated with 21 % O2_Eye_rep_8

value: Eye


title: Free floating negative neurosphere NNI-8 replicate 4

description:
replicate 4
4310479204_D

source_name: Primary neurosphere

value: negative


title: Control_100_Eye_9

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Eye_rep_9


title: Free floating negative neurosphere NNI-1 replicate 2

description:
replicate 2
4310479110_B


title: Free floating positive neurosphere NNI-1 replicate 1

description:
replicate 1
4310479110_A

value: positive


title: Free floating positive neurosphere NNI-1 replicate 3

description:
replicate 3
4310479204_A


title: Control_21_Eye_6

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Eye_rep_6

value: Normoxia (control)


title: Semi-adherent negative neurosphere NNI-4 replicate 4

description:
replicate 4
4329313033_D

value: Glioblastoma multiforme


title: Free floating negative neurosphere NNI-8 replicate 2

description:
replicate 2
4310479110_D

value: Free floating


title: Hypoxia_100_Eye_7

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_7


title: Hypoxia_60_Eye_7

source_name: Hypoxia group_reoxygenated with 60 % O2_Eye_rep_7


title: Hypoxia_21_Eye_7

source_name: Hypoxia group_reoxygenated with 21 % O2_Eye_rep_7


title: Hypoxia_40_Eye_7

source_name: Hypoxia group_reoxygenated with 40 % O2_Eye_rep_7


title: Free floating positive neurosphere NNI-8 replicate 3

description:
replicate 3
4310479204_C


title: Free floating negative neurosphere NNI-1 replicate 4

description:
replicate 4
4310479204_B


title: Hypoxia_40_Brain_7

source_name: Hypoxia group_reoxygenated with 40 % O2_Brain_rep7

value: Brain


title: Control_100_Brain_9

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Brain_rep9


title: Hypoxia_60_Brain_8

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep8


title: Hypoxia_100_Brain_7

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep7


title: Semi-adherent positive neurosphere NNI-4 replicate 1

description:
replicate 1
4329313033_A

value: Primary neurosphere


title: Semi-adherent negative neurosphere NNI-4 replicate 3

description:
replicate 3
4329313033_C


title: Control_21_Brain_6

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Brain_rep6


title: Semi-adherent positive neurosphere NNI-4 replicate 2

description:
replicate 2
4329313033_B


title: Free floating positive neurosphere NNI-8 replicate 1

description:
replicate 1
4310479110_C


title: Hom pool-15 generations 350μM 1,2,4-benzenetriol-replicate 1 Down

city: Berkeley

first: Chris

last: Vulpe

state: Ca

address: 119 Morgan Hall

department: Nutritional Sciences and Toxicology

institute: UC Berkeley

description: Down tag data processing

hyb_protocol: Reactions hybridized overnight to custom-built TAG4 microarrays (Affymetrix)

scan_protocol: After hybridization, arrays were stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix)

data_processing: Robust mean Log2 intensity for replicate features calculated with S-plus/R function. Up and down tags are processed separately and output reported as separate data sets. Note: Platform GPL8633 contains the array design which will be helpful for users who do not want to use our preprocessing strategy.

organism: Saccharomyces cerevisiae

label_protocol: The strain-specific barcodes contained in the DNA were amplified by PCR using a set of biotinylated primers

growth_protocol: Growth in YPD (rich) media, 30 °C, 200 rpm. Measurements of optical density at 595 nm (OD595) to monitor growth

extract_protocol: Cells were collected and genomic DNA was extracted using the YDER kit (Pierce Biotechnology)

treatment_protocol: Chemical treatments incorporated into growth media, 3 concentrations with 3 biological replicates each, for 5 and 15 generations (g) of growth

tag: pool

value: Homozygous deletion mutants

tag: growth stage

value: 15 generations

tag: agent

tag: concentration


title: Control_21_Lung_4

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Lung_rep_4

tag: tissue

value: Lung

tag: age

value: Postnatal day seven


title: Hom pool-15 generations 175μM 1,2,4-benzenetriol-replicate 2 Down

description: Down tag data processing


title: Control_21_Lung_5

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Lung_rep_5


title: Hom pool-15 generations 175μM 1,2,4-benzenetriol-replicate 3 Down

description: Down tag data processing


title: Hom pool-15 generations 350μM 1,2,4-benzenetriol-replicate 2 Down

description: Down tag data processing


title: Hom pool-15 generations 350μM 1,2,4-benzenetriol-replicate 3 Down

description: Down tag data processing


title: Control_21_Lung_2

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Lung_rep_2


title: Control_21_Lung_3

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Lung_rep_3


title: Hypoxia_21_Brain_7

source_name: Hypoxia group_reoxygenated with 21 % O2_Brain_rep7

value: Hypoxia


title: Control_21_Lung_1

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Lung_rep_1


title: Hom pool-15 generations 175μM 1,2,4-benzenetriol-replicate 1 Down

description: Down tag data processing


title: Hom pool-15 generations 87.5μM 1,2,4-benzenetriol-replicate 1 Down

description: Down tag data processing


title: Hom pool-15 generations 87.5μM 1,2,4-benzenetriol-replicate 2 Down

description: Down tag data processing


title: Control_100_Lung_5

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Lung_rep_5


title: Hom pool-15 generations 87.5μM 1,2,4-benzenetriol-replicate 3 Down

description: Down tag data processing


title: Control_100_Lung_8

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Lung_rep_8


title: Hypoxia_60_Lung_10

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_10


title: Control_100_Lung_7

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Lung_rep_7


title: Control_100_Lung_4

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Lung_rep_4


title: Control_100_Lung_6

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Lung_rep_6


title: Hom pool-5 generations 350μM 1,2,4-benzenetriol-replicate 2 Down

description: Down tag data processing

value: 5 generations


title: Hom pool-5 generations 350μM 1,2,4-benzenetriol-replicate 3 Down

description: Down tag data processing


title: Control_100_Lung_3

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Lung_rep_3


title: Free floating DDC neurosphere NNI-1 replicate 4

description:
replicate 4
4672031022_E

source_name: Primary neurosphere

tag: treatment

value: DDC


title: Hom pool-5 generations 350μM 1,2,4-benzenetriol-replicate 1 Down

description: Down tag data processing


title: Control_100_Lung_1

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Lung_rep_1

tag: hypoxia or normoxia group


title: Hypoxia_60_Lung_5

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_5

tag: reoxygenated with


title: Hom pool-5 generations 175μM 1,2,4-benzenetriol-replicate 1 Down

description: Down tag data processing


title: Hom pool-15 generations 2.2mM catechol-replicate 1 Down

description: Down tag data processing

value: catechol


title: Hypoxia_60_Lung_7

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_7


title: Hypoxia_60_Lung_3

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_3


title: Hom pool-5 generations 175μM 1,2,4-benzenetriol-replicate 2 Down

description: Down tag data processing


title: Hypoxia_60_Lung_4

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_4


title: Hom pool-5 generations 175μM 1,2,4-benzenetriol-replicate 3 Down

description: Down tag data processing


title: Hom pool-5 generations 87.5μM 1,2,4-benzenetriol-replicate 2 Down

description: Down tag data processing


title: Hypoxia_40_Lung_6

source_name: Hypoxia group_reoxygenated with 40 % O2_Lung_rep_6


title: Hom pool-5 generations 87.5μM 1,2,4-benzenetriol-replicate 3 Down

description: Down tag data processing


title: Control_100_Lung_2

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Lung_rep_2


title: Hom pool-15 generations 2.2mM catechol-replicate 2 Down

description: Down tag data processing


title: Hom pool-5 generations 87.5μM 1,2,4-benzenetriol-replicate 1 Down

description: Down tag data processing


title: Hom pool-15 generations 1.1mM catechol-replicate 1 Down

description: Down tag data processing


title: Hom pool-15 generations 0.55mM catechol-replicate 3 Down

description: Down tag data processing


title: Hypoxia_60_Lung_2

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_2


title: Hom pool-15 generations 0.55mM catechol-replicate 2 Down

description: Down tag data processing


title: Hypoxia_40_Lung_5

source_name: Hypoxia group_reoxygenated with 40 % O2_Lung_rep_5


title: Hypoxia_60_Lung_6

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_6


title: Hypoxia_40_Lung_2

source_name: Hypoxia group_reoxygenated with 40 % O2_Lung_rep_2


title: Hom pool-15 generations 1.1mM catechol-replicate 3 Down

description: Down tag data processing


title: Hom pool-15 generations 1.1mM catechol-replicate 2 Down

description: Down tag data processing


title: Hypoxia_40_Lung_1

source_name: Hypoxia group_reoxygenated with 40 % O2_Lung_rep_1


title: Hypoxia_60_Lung_1

source_name: Hypoxia group_reoxygenated with 60 % O2_Lung_rep_1


title: Hom pool-5 generations 1.1mM catechol-replicate 1 Down

description: Down tag data processing


title: Hom pool-15 generations 0.55mM catechol-replicate 1 Down

description: Down tag data processing


title: Hom pool-5 generations 0.55mM catechol-replicate 2 Down

description: Down tag data processing


title: Hom pool-5 generations 2.2mM catechol-replicate 3 Down

description: Down tag data processing


title: Hom pool-5 generations 0.55mM catechol-replicate 3 Down

description: Down tag data processing


title: Hom pool-5 generations 2.2mM catechol-replicate 1 Down

description: Down tag data processing


title: Hypoxia_40_Lung_3

source_name: Hypoxia group_reoxygenated with 40 % O2_Lung_rep_3


title: Hypoxia_40_Lung_4

source_name: Hypoxia group_reoxygenated with 40 % O2_Lung_rep_4


title: Hypoxia_21_Lung_2

source_name: Hypoxia group_reoxygenated with 21 % O2_Lung_rep_2


title: Hypoxia_100_Lung_5

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_5


title: Hom pool-15 generations 4mM hydroquinone-replicate 3 Down

description: Down tag data processing

value: hydroquinone


title: Hom pool-5 generations 1.1mM catechol-replicate 2 Down

description: Down tag data processing


title: Hom pool-5 generations 0.55mM catechol-replicate 1 Down

description: Down tag data processing


title: Hom pool-5 generations 2.2mM catechol-replicate 2 Down

description: Down tag data processing


title: Hom pool-5 generations 1.1mM catechol-replicate 3 Down

description: Down tag data processing


title: Hypoxia_21_Lung_6

source_name: Hypoxia group_reoxygenated with 21 % O2_Lung_rep_6


title: Hypoxia_21_Lung_1

source_name: Hypoxia group_reoxygenated with 21 % O2_Lung_rep_1


title: Hypoxia_21_Lung_5

source_name: Hypoxia group_reoxygenated with 21 % O2_Lung_rep_5


title: Hypoxia_21_Lung_3

source_name: Hypoxia group_reoxygenated with 21 % O2_Lung_rep_3


title: Hom pool-15 generations 4mM hydroquinone-replicate 2 Down

description: Down tag data processing


title: Hypoxia_100_Lung_6

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_6


title: Hypoxia_100_Lung_1

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_1


title: Hypoxia_100_Lung_2

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_2


title: Hom pool-15 generations 2mM hydroquinone-replicate 1 Down

description: Down tag data processing


title: Hypoxia_100_Lung_4

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_4


title: Hypoxia_21_Lung_4

source_name: Hypoxia group_reoxygenated with 21 % O2_Lung_rep_4


title: Hom pool-15 generations 1mM hydroquinone-replicate 2 Down

description: Down tag data processing


title: Hom pool-15 generations 1mM hydroquinone-replicate 3 Down

description: Down tag data processing


title: Hypoxia_100_Lung_3

source_name: Hypoxia group_reoxygenated with 100 % O2_Lung_rep_3


title: Hom pool-15 generations 2mM hydroquinone-replicate 2 Down

description: Down tag data processing


title: Control_21_Eye_5

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Eye_rep_5

value: Eye


title: Hom pool-15 generations 1mM hydroquinone-replicate 1 Down

description: Down tag data processing


title: Control_21_Eye_3

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Eye_rep_3


title: Hom pool-15 generations 2mM hydroquinone-replicate 3 Down

description: Down tag data processing


title: Hom pool-15 generations 4mM hydroquinone-replicate 1 Down

description: Down tag data processing


title: Hom pool-5 generations 4mM hydroquinone-replicate 3 Down

description: Down tag data processing


title: Control_21_Eye_4

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Eye_rep_4


title: Control_21_Eye_2

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Eye_rep_2


title: Hom pool-5 generations 4mM hydroquinone-replicate 2 Down

description: Down tag data processing


title: Control_21_Eye_1

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Eye_rep_1


title: Control_100_Eye_8

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Eye_rep_8


title: Control_100_Eye_7

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Eye_rep_7


title: Control_100_Eye_3

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Eye_rep_3


title: Control_100_Eye_4

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Eye_rep_4


title: Control_100_Eye_6

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Eye_rep_6


title: Hom pool-5 generations 4mM hydroquinone-replicate 1 Down

description: Down tag data processing


title: Control_100_Eye_5

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Eye_rep_5


title: Hom pool-5 generations 2mM hydroquinone-replicate 3 Down

description: Down tag data processing


title: Hom pool-15 generations 2.2mM catechol-replicate 3 Down

description: Down tag data processing


title: Control_100_Eye_1

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Eye_rep_1


title: Control_100_Eye_2

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Eye_rep_2


title: Hom pool-15 generations 175μM 1,2,4-benzenetriol-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 1mM hydroquinone-replicate 1 Down

description: Down tag data processing


title: Hom pool-5 generations 1mM hydroquinone-replicate 2 Down

description: Down tag data processing


title: Hom pool-15 generations 350μM 1,2,4-benzenetriol-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 2mM hydroquinone-replicate 2 Down

description: Down tag data processing


title: Hypoxia_60_Eye_2

source_name: Hypoxia group_reoxygenated with 60 % O2_Eye_rep_2


title: Hypoxia_60_Eye_1

source_name: Hypoxia group_reoxygenated with 60 % O2_Eye_rep_1


title: Hom pool-15 generations 175μM 1,2,4-benzenetriol-replicate 2 Up

description: Up tag data processing


title: Hom pool-5 generations 1mM hydroquinone-replicate 3 Down

description: Down tag data processing


title: Hom pool-5 generations 2mM hydroquinone-replicate 1 Down

description: Down tag data processing


title: Hypoxia_60_Eye_4

source_name: Hypoxia group_reoxygenated with 60 % O2_Eye_rep_4


title: Hypoxia_60_Eye_6

source_name: Hypoxia group_reoxygenated with 60 % O2_Eye_rep_6


title: Hom pool-15 generations 175μM 1,2,4-benzenetriol-replicate 1 Up

description: Up tag data processing


title: Hypoxia_60_Eye_5

source_name: Hypoxia group_reoxygenated with 60 % O2_Eye_rep_5


title: Hypoxia_40_Eye_5

source_name: Hypoxia group_reoxygenated with 40 % O2_Eye_rep_5


title: Hypoxia_40_Eye_6

source_name: Hypoxia group_reoxygenated with 40 % O2_Eye_rep_6


title: Hom pool-15 generations 87.5μM 1,2,4-benzenetriol-replicate 3 Up

description: Up tag data processing


title: Hom pool-15 generations 87.5μM 1,2,4-benzenetriol-replicate 2 Up

description: Up tag data processing


title: Hypoxia_60_Eye_3

source_name: Hypoxia group_reoxygenated with 60 % O2_Eye_rep_3


title: Hom pool-15 generations 350μM 1,2,4-benzenetriol-replicate 1 Up

description: Up tag data processing


title: Hypoxia_40_Eye_4

source_name: Hypoxia group_reoxygenated with 40 % O2_Eye_rep_4


title: Hom pool-15 generations 87.5μM 1,2,4-benzenetriol-replicate 1 Up

description: Up tag data processing


title: Hypoxia_40_Eye_3

source_name: Hypoxia group_reoxygenated with 40 % O2_Eye_rep_3


title: Hypoxia_40_Eye_2

source_name: Hypoxia group_reoxygenated with 40 % O2_Eye_rep_2


title: Hom pool-5 generations 350μM 1,2,4-benzenetriol-replicate 2 Up

description: Up tag data processing


title: Hypoxia_21_Eye_6

source_name: Hypoxia group_reoxygenated with 21 % O2_Eye_rep_6


title: Hom pool-5 generations 350μM 1,2,4-benzenetriol-replicate 1 Up

description: Up tag data processing


title: Hypoxia_21_Eye_5

source_name: Hypoxia group_reoxygenated with 21 % O2_Eye_rep_5


title: Hypoxia_40_Eye_1

source_name: Hypoxia group_reoxygenated with 40 % O2_Eye_rep_1


title: Hom pool-5 generations 350μM 1,2,4-benzenetriol-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 87.5μM 1,2,4-benzenetriol-replicate 1 Up

description: Up tag data processing


title: Hypoxia_21_Eye_4

source_name: Hypoxia group_reoxygenated with 21 % O2_Eye_rep_4


title: Hom pool-5 generations 175μM 1,2,4-benzenetriol-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 87.5μM 1,2,4-benzenetriol-replicate 2 Up

description: Up tag data processing


title: Hypoxia_21_Eye_2

source_name: Hypoxia group_reoxygenated with 21 % O2_Eye_rep_2


title: Hypoxia_21_Eye_1

source_name: Hypoxia group_reoxygenated with 21 % O2_Eye_rep_1


title: Hypoxia_21_Eye_3

source_name: Hypoxia group_reoxygenated with 21 % O2_Eye_rep_3


title: Hypoxia_100_Eye_5

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_5


title: Hom pool-5 generations 87.5μM 1,2,4-benzenetriol-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 175μM 1,2,4-benzenetriol-replicate 1 Up

description: Up tag data processing


title: Hypoxia_100_Eye_4

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_4


title: Hom pool-15 generations 1.1mM catechol-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 175μM 1,2,4-benzenetriol-replicate 2 Up

description: Up tag data processing


title: Hom pool-15 generations 2.2mM catechol-replicate 2 Up

description: Up tag data processing


title: Hypoxia_100_Eye_6

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_6


title: Hom pool-15 generations 2.2mM catechol-replicate 1 Up

description: Up tag data processing


title: Hom pool-15 generations 2.2mM catechol-replicate 3 Up

description: Up tag data processing


title: Hypoxia_100_Eye_2

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_2


title: Hypoxia_100_Eye_3

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_3


title: Hypoxia_100_Eye_1

source_name: Hypoxia group_reoxygenated with 100 % O2_Eye_rep_1


title: Hom pool-15 generations 1.1mM catechol-replicate 2 Up

description: Up tag data processing


title: Hom pool-15 generations 1.1mM catechol-replicate 1 Up

description: Up tag data processing


title: Hom pool-15 generations 0.55mM catechol-replicate 3 Up

description: Up tag data processing


title: Control_21_Brain_4

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Brain_rep4


title: Control_21_Brain_5

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Brain_rep5


title: Control_21_Brain_3

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Brain_rep3


title: Hom pool-15 generations 0.55mM catechol-replicate 2 Up

description: Up tag data processing


title: Hom pool-15 generations 0.55mM catechol-replicate 1 Up

description: Up tag data processing


title: Control_21_Brain_2

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Brain_rep2


title: Control_21_Brain_1

source_name: Normoxia (control) group_reoxygenated with 21 % O2_Brain_rep1


title: Hom pool-5 generations 2.2mM catechol-replicate 2 Up

description: Up tag data processing


title: Hom pool-5 generations 2.2mM catechol-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 1.1mM catechol-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 1.1mM catechol-replicate 1 Up

description: Up tag data processing


title: Hom pool-5 generations 1.1mM catechol-replicate 2 Up

description: Up tag data processing


title: Hom pool-5 generations 0.55mM catechol-replicate 2 Up

description: Up tag data processing


title: Hom pool-5 generations 0.55mM catechol-replicate 1 Up

description: Up tag data processing


title: Control_100_Brain_7

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Brain_rep7


title: NLS_Q28_dox+_2

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: RNA was extracted from cells on day 5 after transfection.

hyb_protocol: Hybridization and signal detection of Rat Gene 1.0 ST Arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) in affy library using R and Bioconductor.

organism: Rattus norvegicus

source_name: PC12 NLS-Q28 Dox(+), rep 2

label_protocol: The samples were labeled using the Ambion WT expressio kit (Ambion) as described by the manufacturer.

extract_protocol: Inducible PC12 stable cells were cultured for 5 days with or without Dox and total cellular RNA were isolated by TRIzol (Invitrogen) according to the manufacture’s protocol.

tag: polyq

value: NLS

tag: condition

value: dox+


title: NLS_Q13_dox+_1

source_name: PC12 NLS-Q13 Dox(+), rep 1


title: Hom pool-15 generations 4mM hydroquinone-replicate 1 Up

description: Up tag data processing


title: Control_100_Brain_6

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Brain_rep6

value: Normoxia (control)


title: NLS_Q28_dox+_1

source_name: PC12 NLS-Q28 Dox(+), rep 1


title: NLS_Q28_dox-_1

source_name: PC12 NLS-Q28 Dox(-), rep 1

value: dox-


title: Control_100_Brain_4

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Brain_rep4


title: NLS_Q13_dox+_2

source_name: PC12 NLS-Q13 Dox(+), rep 2


title: Hom pool-5 generations 0.55mM catechol-replicate 3 Up

description: Up tag data processing


title: Hom pool-15 generations 4mM hydroquinone-replicate 2 Up

description: Up tag data processing


title: Control_100_Brain_3

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Brain_rep3


title: NLS_Q28_dox-_2

source_name: PC12 NLS-Q28 Dox(-), rep 2


title: Hom pool-15 generations 2mM hydroquinone-replicate 3 Up

description: Up tag data processing


title: NLS_Q13_dox-_2

source_name: PC12 NLS-Q13 Dox(-), rep 2


title: Control_100_Brain_8

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Brain_rep8


title: Hom pool-15 generations 2mM hydroquinone-replicate 2 Up

description: Up tag data processing


title: Hom pool-15 generations 4mM hydroquinone-replicate 3 Up

description: Up tag data processing


title: NLS_Q13_dox-_1

source_name: PC12 NLS-Q13 Dox(-), rep 1


title: Control_100_Brain_5

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Brain_rep5


title: Hom pool-5 generations 2.2mM catechol-replicate 1 Up

description: Up tag data processing


title: Hom pool-15 generations 2mM hydroquinone-replicate 1 Up

description: Up tag data processing


title: Hom pool-15 generations 1mM hydroquinone-replicate 3 Up

description: Up tag data processing


title: Control_100_Brain_2

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Brain_rep2


title: Hom pool-5 generations 4mM hydroquinone-replicate 3 Up

description: Up tag data processing


title: Hom pool-15 generations 1mM hydroquinone-replicate 1 Up

description: Up tag data processing


title: Hom pool-5 generations 4mM hydroquinone-replicate 1 Up

description: Up tag data processing


title: NES_Q28_dox+_2

source_name: PC12 NES-Q28 Dox(+), rep 2

value: NES


title: Hom pool-15 generations 1mM hydroquinone-replicate 2 Up

description: Up tag data processing


title: Hypoxia_60_Brain_6

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep6

value: Brain


title: Hypoxia_60_Brain_7

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep7


title: Hom pool-5 generations 4mM hydroquinone-replicate 2 Up

description: Up tag data processing


title: Control_100_Brain_1

source_name: Normoxia (control) group_reoxygenated with 100 % O2_Brain_rep1


title: Hypoxia_60_Brain_5

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep5


title: Hom pool-5 generations 1mM hydroquinone-replicate 3 Up

description: Up tag data processing


title: Hom pool-5 generations 1mM hydroquinone-replicate 2 Up

description: Up tag data processing


title: NES_Q28_dox+_1

source_name: PC12 NES-Q28 Dox(+), rep 1


title: Hom pool-5 generations 2mM hydroquinone-replicate 3 Up

description: Up tag data processing


title: Hypoxia_60_Brain_3

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep3


title: Hom pool-15 generations 350μM 1,2,4-benzenetriol-replicate 2 Up

description: Up tag data processing


title: Hom pool-5 generations 2mM hydroquinone-replicate 1 Up

description: Up tag data processing


title: Hom pool-5 generations 2mM hydroquinone-replicate 2 Up

description: Up tag data processing


title: Hypoxia_60_Brain_4

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep4


title: NES_Q28_dox-_2

source_name: PC12 NES-Q28 Dox(-), rep 2


title: Hypoxia_60_Brain_1

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep1


title: Hom pool-5 generations 1mM hydroquinone-replicate 1 Up

description: Up tag data processing


title: NES_Q28_dox-_1

source_name: PC12 NES-Q28 Dox(-), rep 1


title: Hypoxia_60_Brain_2

source_name: Hypoxia group_reoxygenated with 60 % O2_Brain_rep2


title: NES_Q13_dox+_1

source_name: PC12 NES-Q13 Dox(+), rep 1


title: NES_Q13_dox-_2

source_name: PC12 NES-Q13 Dox(-), rep 2


title: Hypoxia_21_Brain_6

source_name: Hypoxia group_reoxygenated with 21 % O2_Brain_rep6


title: Hypoxia_40_Brain_4

source_name: Hypoxia group_reoxygenated with 40 % O2_Brain_rep4


title: Hypoxia_40_Brain_6

source_name: Hypoxia group_reoxygenated with 40 % O2_Brain_rep6


title: undivided_rep6

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: Biotinylated cDNA was hybridized overnight with Affymetrix U133_Plus_2.0 arrays using conditions recommended by NuGEN. After washing, arrays were stained with SAPE followed by signal enhancement with anti-SAPE antibody as recommended by Affymetrix.

scan_protocol: Phycoerythrin fluorescence was quantified with an Affymetrix scanner, and Affymetrix Command Console software was used to generate cel files from the raw scan data.

data_processing: Cel files were quantile-normalized with the GC-RMA method using the open-source gcrma Bioconductor package (R programming language).

source_name: undivided B cells

label_protocol: Total RNA was used to prepare biotinylated cDNA with the WT-Ovation Pico kit as recommended by the kit manufacturer (NuGEN).

growth_protocol: Freshly isolated CD27+ IgG enriched human peripheral blood Bc were cultured in the presence of CpG 2006 (10 ng/ml, Oligos, etc., Wilsonville, OR), plus recombinant human cytokines IL-2 (20 IU/ml), IL-10 (50 ng/ml), IL-15 (10 ng/ml) (all from BD Biosciences, San Diego, CA), and recombinant human BAFF (75 ng/ml, Chemicon, Temecula, CA) PC-L medium (IMDM medium, lacromin (50mg/ml, Seracare, Milford, MA), insulin (5mg/ml, Sigma-Aldrich, St. Louis, MO), penicillin/streptomycin (1x, Invitrogen, Carlsbad, CA), gentamicin (15mg/ml, Invitrogen), heat inactivated fetal bovine serum (10% v/v, Invitrogen), normocin (0.1% v/v, Invivogen, San Diego, CA) in round-bottomed 96-well plates (BD Biosciences, San Diego, CA). All cells were cultured at 37 C, 5% CO2.

extract_protocol: Immediately after collection, sorted cells were lysed in RLT buffer and passed through a Qiashredder column (both from Qiagen, Germantown, MD) and snap frozen in liquid nitrogen. Samples were stored at -70C until RNA extraction. RNA was extracted using the RNeasy Micro Kit with on-column DNAse as recommended by the manufacturer (Qiagen).

treatment_protocol: CFSE-stained cells were harvested, washed, and counted. The cells were stained with Live/Dead Violet Invitrogen, Carlsbad, CA), washed and stained with anti-CD27-APC-H7 antibody (BD Bioscience, San Diego, CA) on ice. FACS cell sorts were performed on live cells.

value: peripheral blood

value: undivided B cells

value: low

tag: divided in vitro

value: no


title: CD27_high_rep6

source_name: CD27_high_proliferating B cells

value: proliferating B cells

value: high

value: yes


title: Hypoxia_40_Brain_3

source_name: Hypoxia group_reoxygenated with 40 % O2_Brain_rep3

value: Postnatal day seven

value: Hypoxia


title: NES_Q13_dox-_1

source_name: PC12 NES-Q13 Dox(-), rep 1


title: Hypoxia_40_Brain_5

source_name: Hypoxia group_reoxygenated with 40 % O2_Brain_rep5


title: CD27_low_rep6

source_name: CD27_low_proliferating B cells


title: CD27_high_rep5


title: Hypoxia_40_Brain_2

source_name: Hypoxia group_reoxygenated with 40 % O2_Brain_rep2


title: NES_Q13_dox+_2

source_name: PC12 NES-Q13 Dox(+), rep 2


title: CD27_low_rep5


title: Hypoxia_21_Brain_5

source_name: Hypoxia group_reoxygenated with 21 % O2_Brain_rep5


title: undivided_rep5


title: Hypoxia_40_Brain_1

source_name: Hypoxia group_reoxygenated with 40 % O2_Brain_rep1


title: CD27_high_rep4


title: Hypoxia_21_Brain_3

source_name: Hypoxia group_reoxygenated with 21 % O2_Brain_rep3


title: CD27_high_rep3


title: CD27_low_rep3


title: Hypoxia_21_Brain_2

source_name: Hypoxia group_reoxygenated with 21 % O2_Brain_rep2


title: undivided_rep4


title: undivided_rep3


title: Hypoxia_21_Brain_4

source_name: Hypoxia group_reoxygenated with 21 % O2_Brain_rep4


title: Hypoxia_100_Brain_6

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep6


title: Art Replicate 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
7438_Art 3
Mouse ID: Art.1 INV4
Gene expression from Artemis-deficient v-abl-transformed pre-B cells.

hyb_protocol: Fragmented RNA was hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed using the EukGE-WS2v5 protocol of the Affymetrix Fluidics Station FS450 for antibody amplification.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Operating Software (GCOS; Version 1.4.0.036).

label_protocol: One microgram of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol. Fifteen micrograms of amplified biotin-cRNAs were fragmented.

growth_protocol: Cells were maintained in suspension in Dulbecco's Modified Eagle Medium (DMEM), high glucose (Gibco BRL 11960-077) supplemented with 10% fetal bovine serum, 1X Sodium Pyruvate (Gibco BRL 11360-070), 1X Non-Essential Amino Acids (Gibco BRL 11140-050), 1X L-Glutamine (Gibco BRL 25030-081), and 2 μl of beta-mercaptoethanol.

extract_protocol: RNA was isolated using Qiagen RNeasy technology following the manufacturer’s instructions, including the addition of DNase.

treatment_protocol: Cells treated with STI571 were passaged with 3 μM STI-571 (Imatinib Mesylate) added to the media, incubated for 48 hr and then harvested.

tag: genotype

value: Artemis-deficient

value: G1-phase pre-B cells


title: Hypoxia_100_Brain_5

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep5


title: Hypoxia_21_Brain_1

source_name: Hypoxia group_reoxygenated with 21 % O2_Brain_rep1


title: Art Replicate 1

description:
7436_Art 1
Mouse ID: Art 2.1
Gene expression from Artemis-deficient v-abl-transformed pre-B cells.


title: CD27_high_rep2


title: Rag Replicate 3

description:
7435_Rag_rep3
Mouse ID: R2K Bcl.3
Gene expression from RAG-2-deficient v-abl-transformed pre-B cells.

tag: sample type

value: control


title: CD27_low_rep2


title: Art Replicate 2

description:
7437_Art 2
Mouse ID: Art 5.1
Gene expression from Artemis-deficient v-abl-transformed pre-B cells.


title: Rag Replicate 2

description:
7434_420_Rag_rep_2
Mouse ID: R2K Bcl.2
Gene expression from RAG-2-deficient v-abl-transformed pre-B cells.


title: CD27_high_rep1


title: Hypoxia_100_Brain_4

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep4


title: Hypoxia_100_Brain_3

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep3


title: undivided_rep2

source_name: undivided B cells


title: CD27_low_rep1


title: F1_leaf_floated_0.1%Tween20_0.1%acetone_rep3

city: York

first: David

last: Wortley

state: North Yorkshire

address: Wentworth Way

institute: University of York

hyb_protocol: Affymetrix Eukaryotic Sample Processing protocol followed - 16 hours at 45oC in rotating hybridisation oven

scan_protocol: Affymetrix GeneChip Command Console Scan Control 1.1.0.845. Affymetrix 450 Scanner.

data_processing: Affymetrix Expression Console software v1.1. MAS5.

organism: Arabidopsis thaliana

source_name: leaf tissue, floated on 0.1% Tween 20, 0.1% acetone, 4 hours

label_protocol: Affymetrix Eukaryotic Sample Processing protocol followed - biotin labelling of antisense cRNA

growth_protocol: Seeds were chilled for 72 hours at 4 °C prior to sowing on F2 compost and maintaining in growth rooms set to a 16-hour day length, 20 °C.

extract_protocol: Frozen tissue was ground to a fine powder in liquid nitrogen and total RNA extracted using the commercially available Rneasy mini kit (Qiagen).

treatment_protocol: For each replicate, ten leaves were floated on a solution containing 0.1 % Tween 20 + 0.1 % acetone and maintained for 4 hours in growth room conditions. After 4 hours had elapsed tissue was harvested, flash frozen using liquid nitrogen and stored at -80 °C.

tag: ecotype

tag: transgene

value: leaf tissue


title: Hypoxia_100_Brain_1

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep1

tag: strain


title: Hypoxia_100_Brain_2

source_name: Hypoxia group_reoxygenated with 100 % O2_Brain_rep2


title: Rag Replicate 1

description:
7433_420_Rag_rep_1
Mouse ID: R2K Bcl.1
Gene expression from RAG-2-deficient v-abl-transformed pre-B cells.

tag: cell type


title: F1_leaf_floated_0.1%Tween20_0.1%acetone_rep1


title: F1_leaf_floated_0.1%Tween20_0.1%acetone_rep2


title: MPZ-Tfam Knockout - rep2

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

hyb_protocol: 750ng of each aRNA in water (10ul) was suspended in Illumina “HYB” buffer (20ul) and heated to 65C for five minutes, then allowed to cool to room temperature.  The samples were applied to HumanHT12v3 Expression Beadchips and hybridized at 58C for 16-20 hours at high humidity.  Arrays were washed according to Illumina standard protocol.  Immobilized, biotinylated aRNAs were then detected by staining with cy3 Steptavidin (1ug cy3-SA per 1 ml of Illumina “Block E1”) for 10 minutes at room temperature.  Arrays were washed and dried according to Illumina standard protocol.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader.  Laser power and PMT voltage were kept constant for Cy3 scans.

data_processing: Images were quantitated by Illumina Beadscan, v3.  Quantitated data was imported into Beadstudio software.  On-slide spot replicates were averaged by Beadstudio and individual spot data was reported

source_name: sciatic nerve

label_protocol: RNA samples were labeled with biotin according to Manufacturer's instructions.

extract_protocol: RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) as per manufacturer’s protocol.

value: sciatic nerve

value: 2 months

value: MPZ-Tfam KO