title: KO VSV infected, biological replicate 3

first: Melissa

middle: B

last: Uccellini

address: 1468 Madison Ave

institute: Mt Sinai School of Medicine

description: Gene expression data

hyb_protocol: 16 hr hybridization

scan_protocol: 488 nm, 570 nm, Affymetrix Genechip Scanner

data_processing: The data were processed using MAS5. Genepattern software filtered the MAS5 values for the genes that were significant. These data are on the Series record.

source_name: Mouse whole brain

growth_protocol: 8-week old male mice were infected intranasally with 107 pfu of VSV-Indiana strain. At 5 days post-infection mice were perfused and whole brain was harvested for RNA extraction.

treatment_protocol: Brains from 3 mice were pooled into 1 sample and samples were run in triplicate (total of 9 mice per condition)

value: whole brain

tag: age

value: 8 weeks, 5 days

tag: infection

value: 107 pfu of VSV-Indiana strain


title: Panc-10.05 untreated, replica 2

status: Public on Apr 04 2013

type: RNA

city: San Francisco

first: Stephan

middle: Christoph

last: Gysin

state: California

address: 1450 3rd Street

department: HDFCCC

country: USA

institute: UCSF

hyb_protocol: Fragmented amplified cDNA was hybridized to AffymetrixHG-U133A 2.0 gene chips according to manufacturer's protocols (Affymetrix).

scan_protocol: Scanning was performed according to Affymetrix protocols

data_processing: Raw hybridization data was preprocessed using Affymetrix Expression Console software (program-id = 1.3.0.187).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Panc-10.05 untreated

label_protocol: 2ug of total RNA was converted to cDNA, amplified, and biotinylated using the Message Amp II mRNA amplification kit from Ambion

growth_protocol: human pancreatic cancer cell lines were grown in culture in 3 replicas for vehicle control and 3 replicas for treatment

extract_protocol: Cells were collected and RNA was extracted using Rneasy from QIAGEN

treatment_protocol: Cells were treated either with vehicle or 2mM CI-1040 for 24 hours

tag: cell line

tag: cell type

value: human pancreatic cancer cells

tag: treated with

value: vehicle control


title: KO uninfected, biological replicate 3

city: New York

state: NY

description: Gene expression data

label: biotin

organism: Mus musculus

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

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

tag: tissue

tag: strain

tag: genotype/variation


title: mRNA expression in androgenetic embryonic stem cells, rep 2

city: Cheongju

first: Nam-Hyung

last: Kim

state: Chungbuk

address: Gaeshin-dong

country: South Korea

institute: Chungbuk National University

description:
Sample 2
Androgenetic embryonic stem cell: aESC (AN).

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina MouseRef-8 Expression BeadChip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner.

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected gene signal values were transformed by logarithm and normalized by the quantile method.

source_name: Mouse androgenetic embryonic stem cell (aESC)

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

extract_protocol: Total RNA extraction was performed with the mirVana extraction kit (Ambion).

tag: gender

value: female and male

value: androgenetic embryonic stem cells

tag: chromosomes contained

value: both X and Y

tag: passage


title: mRNA expression in parthenogenetic embryonic stem cells, rep 2

description:
Sample 5
Parthenogenetic embryonic stem cell (pESC, PA).

source_name: Mouse parthenogenetic embryonic stem cell (pESC)

value: female

value: parthenogenetic embryonic stem cells


title: WT VSV infected, biological replicate 2

description: Gene expression data

value: wild type


title: WT VSV infected, biological replicate 3

description: Gene expression data


title: Panc-3.27 treated, replica 2

source_name: Panc-3.27 treated

value: 2mM CI-1040 for 24 hours


title: mRNA expression in androgenetic embryonic stem cells, rep 1

description:
Sample 1
Androgenetic embryonic stem cell: aESC (AN).


title: KO VSV infected, biological replicate 1

description: Gene expression data


title: mRNA expression in fertilized embryonic stem cells, rep 3

description:
Sample 8
Fertilized embryonic stem cell (fESC, FE).

source_name: Mouse fertilized embryonic stem cell (fESC)

value: fertilized embryonic stem cells


title: Panc-3.27 treated, replica 1


title: KO uninfected, biological replicate 2

description: Gene expression data


title: KO VSV infected, biological replicate 2

description: Gene expression data


title: WT VSV infected, biological replicate 1

description: Gene expression data


title: Panc-3.27 untreated, replica 3

source_name: Panc-3.27 untreated


title: WT uninfected, biological replicate 3

description: Gene expression data


title: Panc-3.27 untreated, replica 2


title: WT uninfected, biological replicate 1

description: Gene expression data


title: KO uninfected, biological replicate 1

description: Gene expression data


title: Het IR-host_50

city: Berkeley

first: David

middle: H

last: Nguyen

state: CA

address: 1 Cyclotron Road, MS-977

department: Cancer & DNA Damage Response

institute: Lawrence Berkeley National Laboratory

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_7

hyb_protocol: 12.5 micrograms of fragmented cRNA was hybridized for 16 hr to the Affymetrix MG 430 2.0 arrays using GeneChip Hybridization Oven 640 and Genechip® fluidics station FS 450, following standard Affymetrix protocols.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Agilent GeneSpring GX10 program. No further adjustments were made to the data in the table.

source_name: Total RNA of p53null mammary tumor, TGFb-Het-Irradiated host

label_protocol: 100 ng of total RNA were used to prepare cRNA following the Affymetrix 3’IVT Express Kit labeling protocol

growth_protocol: p53null tumors developed from p53null mammary fragments that were orthotoically transplanted into the inguinal mammary fat pads of female host mice that had their endogenous epithelium removed at 3wks of age.

extract_protocol: Total RNA was extracted using Trizol Reaget (Invitrogen), according to manufacturer's instructions.

treatment_protocol: Host mice were either irradiated or not, three days before transplantation.

value: BALB/c

value: transplanted p53null mammary tumor

tag: host genotype/variation

value: irradiated TGFb1 heterozygote


title: Het IR-host_55

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_8


title: Het IR-host_47

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_5


title: Het IR-host_49

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_6


title: WT uninfected, biological replicate 2

description: Gene expression data


title: AML Patient 11

city: Cambridge

first: Weng Khong

last: Lim

state: Cambridgeshire

address: Tennis Court Road

country: United Kingdom

institute: Cambridge Systems Biology Centre

hyb_protocol: The cRNA is hybridised to the Illumina beadchip following the Direct Hybridisation assay

scan_protocol: Illumina bead array scanner was used according to manufacturer's instructions

data_processing: Beadsummary data was loaded into the R environment and processed using the beadarray package. VSN normalisation was performed. Only probes common between HumanHT-12 V4.0 and HumanWG-6 v3.0 were retained and considered for further analysis.

source_name: AML patient blasts

label_protocol: RNA samples are amplified using the TotalPrep 96-RNA amplification kit from Ambion (Applied Biosystems). RNA is converted into cDNA, and amplified by In Vitro Transcription (IVT) to generate biotin-labelled cRNA.

extract_protocol: RNA extraction was performed using Trizol(r) according to manufacturer's instructions

value: Female

tag: status(dd(dead)/al(alive))

tag: overall survival (months)

tag: karyotype

tag: wbc

tag: fab subtype

tag: npm1 mutation

value: yes

value: no

tag: secondary?

value: NO


title: Panc-2.13 treated, replica 3

source_name: Panc-2.13 treated

tag: cell line

value: human pancreatic cancer cells


title: AML Patient 17

tag: age

value: AL


title: Panc-2.13 treated, replica 2

tag: cell type

tag: treated with


title: Het IR-host_35

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_3

tag: strain

tag: tissue


title: Panc-2.13 treated, replica 1


title: AML Patient 1

tag: gender

value: DD

value: YES


title: Panc-2.13 untreated, replica 3

source_name: Panc-2.13 untreated

value: vehicle control


title: Panc-3.27 untreated, replica 1


title: Normal CD34 control 3

source_name: Donor CD34 HSCs


title: Normal CD34 control 1


title: AML Patient 10

value: Male

value: TKD


title: Het IR-host_4

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_4


title: AML Patient 16

value: ITD


title: Het IR-host_51

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_18


title: Het IR-host_26

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_2


title: AML Patient 25


title: Panc-2.13 untreated, replica 1


title: Het IR-host_1

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_1


title: HP1 wa191 S2-DRSC 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: HP1 wa191 S2 ChIP expt.280 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

tag: developmental stage

value: late embryonic stage

tag: Sex


title: HP1 wa191 S2-DRSC D.melanogaster Input Rep2

source_name: HP1 wa191 S2 Input expt.240 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: AML Patient 8

value: abnormal chrom 3 (?q26) + marker


title: HP1 wa191 S2-DRSC D.melanogaster ChIP Rep2

source_name: HP1 wa191 S2 ChIP expt.281 channel_1


title: Het IR-host_42

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_17

value: BALB/c

value: transplanted p53null mammary tumor

tag: host genotype/variation


title: Panc-2.13 untreated, replica 2


title: HP1 wa191 S2-DRSC D.melanogaster Input Rep1

source_name: HP1 wa191 S2 Input expt.85 channel_1


title: HPAF_II treated, replica 3

source_name: HPAF_II treated

value: 2mM CI-1040 for 24 hours


title: H3K9me2 antibody2 L3 Nuclei SexedFemaleJilMutant-Heterozygous D.melanogaster ChIP Rep2

source_name: H3K9me2 antibody2 L3 Nuc. SexedFJilMutant-HZ ChIP expt.1945 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: Sexed Female Jil mutant-heterozygous(official name :JIL-1z2)

value: 3rd Instar Larvae Sexed Female

tag: genotype

value: Jil-1 z2/TM3 Ser-GFP

value: Female

tag: transgene

value: deletion


title: HPAF_II treated, replica 1

value: human pancreatic cancer cells


title: Het IR-host_34

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_16

value: irradiated TGFb1 heterozygote


title: AML Patient 12

tag: status(dd(dead)/al(alive))

tag: overall survival (months)

tag: karyotype

value: no

value: NO


title: HPAF_II treated, replica 2


title: AML Patient 18

value: DD

tag: wbc

tag: fab subtype

tag: npm1 mutation

value: yes


title: Het IR-host_33

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_15


title: AML Patient 24

value: Male

tag: age

tag: secondary?


title: Het IR-host_29

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_13


title: AML Patient 5

value: AL

value: inv 16

value: TKD


title: AML Patient 2

value: YES


title: H3K9me2 antibody2 L3 Nuclei SexedFemaleJilMutant-Heterozygous D.melanogaster Input Rep2

source_name: H3K9me2 antibody2 L3 Nuc. SexedFJilMutant-HZ Input expt.1909 channel_1


title: H3K9me2 antibody2 L3 Nuclei SexedFemaleJilMutant-Heterozygous D.melanogaster Input Rep1

source_name: H3K9me2 antibody2 L3 Nuc. SexedFJilMutant-HZ Input expt.1908 channel_1


title: Het IR-host_23

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_12

value: BALB/c

value: transplanted p53null mammary tumor


title: HPAF_II untreated, replica 2

source_name: HPAF_II untreated

tag: cell line

tag: cell type

tag: treated with

value: vehicle control


title: HPAF_II untreated, replica 3


title: HPAF_II untreated, replica 1


title: H3K9me2 antibody2 L3 Nuclei SexedFemaleJilMutant-Heterozygous D.melanogaster ChIP Rep1

source_name: H3K9me2 antibody2 L3 Nuc. SexedFJilMutant-HZ ChIP expt.1943 channel_1

tag: strain

value: Sexed Female Jil mutant-heterozygous(official name :JIL-1z2)

value: 3rd Instar Larvae Sexed Female

value: Jil-1 z2/TM3 Ser-GFP


title: AML Patient 15

tag: gender

value: ITD


title: Het IR-host_32

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_14

tag: tissue

value: irradiated TGFb1 heterozygote


title: Panc-8.13 treated, replica 3

source_name: Panc-8.13 treated

value: human pancreatic cancer cells

value: 2mM CI-1040 for 24 hours


title: Normal CD34 control 5


title: Het IR-host_7

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_11

tag: host genotype/variation


title: HP4 Q4072 S2-DRSC HP4 RNAi D.melanogaster ChIP Rep2

source_name: HP4 Q4072 S2 HP4 RNAi ChIP expt.2090 channel_1

extract_protocol:
The template for the dsRNA synthesis was PCR amplified from Drosophila genomic DNA using specific primers extended with 5? T7-promoter tails. The sequence of the T7-promoter tails is as follows: 5?- CTAATACGACTCACTATAGGGAG-3?. The amplicon was selected such that it is contained within single exon. Following PCR the template was purified using PCR purification Kit from Qiagen. 2.5ug of purified template was used to synthesize dsRNA with Ribomax T7 RNA transcription kit from Promega. The dsRNA was precipitated with ethanol, dissolved in 300ul of pure water, denatured by heating to 65C for 30min and re-annealed by slow cooling to room temperature.2x10^6cells were treated with 50ug of dsRNA in 25cm2 T-flask for 1 hour in serum-free Schneider?s media. They were further brought up 6ml of Schneider?s media supplemented with 10% FBS and grown to confluence (~4 days). The cells were passaged to a 75cm2 T-flask and treated the second time with 200ug of dsRNA as described above. Following the treatment the cells were grown to confluence in 15ml Schneider?s media. 1ml of resulted culture was taken for preparation of nuclear and cytoplasmic protein extracts and the rest was in vivo crosslinked with formaldehyde. The protocol typically yields about 7x10^7 crosslinked cells, which is enough for about 7 ChIPs. And the RNAi treated cells were treated with formaldehyde as in normal cultured cell.
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

tag: developmental stage

value: late embryonic stage

tag: Sex


title: HP4 Q4072 S2-DRSC HP4 RNAi D.melanogaster ChIP Rep1

source_name: HP4 Q4072 S2 HP4 RNAi ChIP expt.1938 channel_1

value: Male


title: Panc-8.13 treated, replica 2


title: Panc-8.13 treated, replica 1


title: Het IR-host_56

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_9

source_name: Total RNA of p53null mammary tumor, TGFb-Het-Irradiated host


title: Het Sham-IR-host_15

description: mouse_p53null-mammary-tumor_TGFb-Het_sham-irradiated host_repeat_6

source_name: Total RNA of p53null mammary tumor, TGFb-Het-Sham host

value: sham-irradiated TGFb1 heterozygote


title: AML Patient 20

source_name: AML patient blasts

value: Female

tag: status(dd(dead)/al(alive))

value: AL

value: add 11 (p15) in 6/20 chromosomes

value: yes

value: no

value: NO


title: HP4 Q4072 S2-DRSC HP4 RNAi D.melanogaster Input Rep2

source_name: HP4 Q4072 S2 HP4 RNAi Input expt.2080 channel_1


title: HP4 Q4072 S2-DRSC HP4 RNAi D.melanogaster Input Rep1

source_name: HP4 Q4072 S2 HP4 RNAi Input expt.1923 channel_1


title: AML Patient 4

tag: overall survival (months)


title: Panc-8.13 untreated, replica 3

source_name: Panc-8.13 untreated

value: vehicle control


title: SU-HW HB S2-DRSC SuHw RNAi D.melanogaster ChIP Rep2

source_name: SU-HW HB S2 SuHw RNAi ChIP expt.1324 channel_1


title: Het Sham-IR-host_38

description: mouse_p53null-mammary-tumor_TGFb-Het_sham-irradiated host_repeat_5

value: BALB/c

value: transplanted p53null mammary tumor


title: Het IR-host_6

description: mouse_p53null-mammary-tumor_TGFb-Het_Irradiated host_repeat_10


title: AML Patient 3

value: DD

tag: karyotype

value: YES


title: Normal CD34 control 7

source_name: Donor CD34 HSCs

tag: wbc


title: SU-HW HB S2-DRSC SuHw RNAi D.melanogaster ChIP Rep1

source_name: SU-HW HB S2 SuHw RNAi ChIP expt.1292 channel_1


title: Het Sham-IR-host_30

description: mouse_p53null-mammary-tumor_TGFb-Het_sham-irradiated host_repeat_4


title: Panc-8.13 untreated, replica 2

value: human pancreatic cancer cells


title: SU-HW HB S2-DRSC SuHw RNAi D.melanogaster Input Rep2

source_name: SU-HW HB S2 SuHw RNAi Input expt.1322 channel_1


title: Het Sham-IR-host_19

description: mouse_p53null-mammary-tumor_TGFb-Het_sham-irradiated host_repeat_2


title: SU-HW HB S2-DRSC SuHw RNAi D.melanogaster Input Rep1

source_name: SU-HW HB S2 SuHw RNAi Input expt.1302 channel_1


title: Normal CD34 control 4

tag: fab subtype


title: Panc-8.13 untreated, replica 1


title: CFPAC-1 treated, replica 3

source_name: CFPAC-1 treated

value: 2mM CI-1040 for 24 hours


title: AML Patient 6

value: CML blast crisis

tag: npm1 mutation


title: CFPAC-1 treated, replica 2


title: Het Sham-IR-host_52

description: mouse_p53null-mammary-tumor_TGFb-Het_sham-irradiated host_repeat_3


title: Het Sham-IR-host_58

description: mouse_p53null-mammary-tumor_TGFb-Het_sham-irradiated host_repeat_1


title: WT IR-host_59

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_23

source_name: Total RNA of p53null mammary tumor, WT-Irradiated host

value: irradiated wild-type


title: CFPAC-1 untreated, replica2

source_name: CFPAC-1 untreated


title: CFPAC-1 treated, replica 1


title: WT IR-host_57

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_22


title: CFPAC-1 untreated, replica3


title: WT IR-host_5

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_20


title: Panc-6.03 treated, replica 3

source_name: Panc-6.03 treated


title: T cell normal control JHR H3K27me3

description: Enrichment analysis of ChIP antibody-bound DNA vs input DNA

hyb_protocol: The labelled samples were dissolved in 24ul water, then 30ul of hybridisation buffer (Agilent) was added with a further blocking agent (Agilent). The sample was then hybridised onto the custom designed chips. To optimise hybridisation to the arrays, the Slidebooster system (Implen) was used, at 65C for 16 hours.

scan_protocol: Arrays were scanned using the Agilent DNA Microarray Scanner and data extracted using Agilent Feature Extraction software version 10.5.1.1.

data_processing: Microarray raw values were loaded into the R Bioconductor platform and preprocesses using the limma package. Median normalisation was performed on a per-array basis with the background correction performed using the “normexp” method.

label: AlexaFluor 3

source_name: Normal donor T cells

label_protocol: The sample was precipitated with 100% ethanol and 0.3M sodium acetate pH 5.5 and labelled. This was performed using the Invitrogen Bioprime for Agilent array based Comparative Genomic Hybridisation system. The fluorophores used are Alexa Fluor 3® and AlexaFluor 5®, similar to Cy3 and 5, but providing higher signal to noise ratios on the array. Alexafluor 5® is said to be a stronger dye than Alexafluor 3®, and therefore to minimise false positive results the input samples are labelled with the stronger dye.  1-3ug of amplified DNA was combined with 4.4 ul of 5mM EDTA and the appropriate Alexafluor dye labelled nucleotide master mix.  The sample was then heated to 95C for 5 minutes and cooled on ice for 5 minutes.  3ul of Exo-klenow, a mutant form of the Klenow fragment of DNA polymerase was added, and the samples were incubated at 37C overnight.  After purification using Purelink™ purification columns (Invitrogen) the dye incorporation was checked using a nanodrop ND-1000.  7-12 ug of each labelled sample was obtained, with a dye incorporation of 30-40 pmol/ug.  The labelled corresponding IP and input samples were combined and 50ug human Cot-1(Invitrogen) DNA added.   Cot-1 DNA® is placental DNA, predominantly 50 to 300 bp in size and enriched for repetitive DNA sequences.  The samples were precipitated with 100% ethanol and 0.3M sodium acetate pH 5.5.  They were centrifuged at 13,200 rpm for 20 minutes at 4C, the supernatant removed and then washed in 70% ethanol at room temperature.  The pellet was air dried, and either hybridised immediately or stored at -80C.

extract_protocol: Assays were performed by modification of a published technique. After 24 hours culture in RPMI supplemented with 10% FCS and 2mM L-glutamine,between 3 million and 30 million cells were transferred to serum-free media then treated with 1% formaldehyde for 10 minutes to cross-link the histone protein to the DNA. The reaction was terminated by the addition of glycine to a concentration of 0.125M.  After washing with cold PBS the cell pellets were resuspended in cell lysis buffer (10mM NaCl, 10mMol Tris pH 8.0, 0.2% NP40 alternative (Cambiochem), plus protease inhibitors 10 mM sodium butyrate (Sigma), 1ug/ml leupeptin (Sigma) and 50ug/ml PMSF (Sigma), and incubated on ice for 10 minutes.  Nuclei were recovered by centrifugation at 2000 rpm at 4C and lysed in nuclei lysis buffer (50mM Tris pH 8.1, 10 mM EDTA, 1% SDS and protease inhibitors as previous).  The chromatin, at a concentration of 1 million cells per 30ul, was then sonicated for 5-9 minutes in 30s pulses using a Bioruptor sonicator. The efficiency of sonication, and therefore the size of the fragments, varied markedly between different cell types and patients, and had to be optimised for individual samples.  The size of the sonicated DNA fragments was assessed by running an aliquot of the input DNA on a 1% agarose gel containing ethidium bromide (Sigma) at a concentration of 1 in 30,000. If the range of fragment sizes was outside the optimal range of 300-800 bp, then further sonication was applied. The cells were then diluted in IP dilution buffer (20mM Tris pH 8.1, 2mM EDTA, 150 mM NaCl, 1% Triton X100 (Sigma), 0.001% SDS and protease inhibitors, as previous). Input chromatin equivalent to 0.5 x 10^6 - 1 x 10^6 cells was stored at -20C.  The remaining chromatin was divided into 3 aliquots, and incubated with antibody at 4C on a rolling platform overnight.  The antibodies used were to acetylated H3K9(Upstate), trimethylated H3K27 (Upstate) both at 5ul per 10^7 cells, and anti-rabbit IgG (Sigma) 7ul per 10^7 cells. To collect the immunoprecipitated complexes, Protein G-agarose beads (Roche Diagnostics) were added and incubated on a rolling platform for 3 hours at 4C.  The protein G pellets were then washed twice with 20mM Tris pH8.1, 2mM EDTA, 50mM NaCl, 1% Triton X-100 and 0.1% SDS followed by one wash with 10mM Tris pH8.1, 1mM EDTA, 0.25M LiCl, 1% NP40 and 1% sodium deoxycholate monohydrate (Sigma). After 2 washes with TE the DNA-protein-antibody complexes were eluted with 100mM NaHCO3 and 1% SDS. The complexes were treated with RNaseA (1ug) and the cross links were reversed by the addition of 5MNaCl to a final concentration of 0.3M and heating at 67C overnight.  60 ug proteinase K was then added and incubated at 45C for 2 hours, prior to purification using the QIAquick PCR cleanup kit (Qiagen) and eluted in 30 ul of water.

treatment_protocol: T cells were obtained from peripheral blood of healthy donors. Cells were processed to obtain the mononuclear fraction by density gradient centrifugation using Histopaque (Sigma) as previously described, and the T cell fraction obtained by positive selection with magnetic CD3 beads (Miltenyi Biotech). Cells were frozen, thawed and cultured using the same conditions applied to AML patient samples.

tag: chip antibody

value: H3K27me3 anti trimethyl histone H3 (lys27) - Millipore cat # 07-449, lot #DAM1703508 and DAM 1387952

tag: age

tag: status

tag: flt3 mutation

label: AlexaFluor 5

value: Input DNA


title: T cell normal control JHR H3K9ac

value: H3K9ac (recognizes H3K9/K14 Acetylation):Millipore 06-599 lot# JBC1349702

tag: secondary?


title: Panc-6.03 treated, replica 2

tag: cell line

tag: cell type

tag: treated with


title: 450mg/kg_mr40

first: Daniel

last: Rohle

address: 1275 York Avenue

department: The Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description:
TS603 R132H Glioma Xenograft Experiment 2
Gene Expression Data from xenografts

hyb_protocol: cRNA was hybridized according to standard Affymetrix protocol.

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

data_processing: The data was analzyed using Partek Genomics Suite and Treeview software

source_name: Oligodendroglioma

label_protocol: 200ng of your samples were amplified/labeled using the Affymetrix 3’IVT Express kit for 4 hours.

growth_protocol: SCID mice were injected subcutaneously with 10^6 glioma cells, which were suspended in 100 mL of a 50:50 mixture of growth media and Matrigel (BD #356237). Once tumors had reached a measurable size, mice were randomized into the indicated treatment groups.

extract_protocol: Total RNA was extracted by Qiagen RNeasy Lipid Tissue kit according to the manufactuer's protocol.

treatment_protocol: Mice were treated with the indicated treated once a day by gavage.

tag: mutation

tag: treatment

tag: tissue

value: Oligodendroglioma


title: CFPAC-1 untreated, replica1


title: 450mg/kg_mr34


title: WT IR-host_21

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_19

tag: strain

tag: host genotype/variation


title: WT IR-host_54

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_21


title: 450mg/kg_mr38


title: Panc-6.03 untreated, replica 2

source_name: Panc-6.03 untreated


title: Panc-6.03 treated, replica 1


title: T cell normal control CP H3K9ac

tag: gender

tag: overall survival (months)

tag: karyotype


title: 450mg/kg_mr36


title: 450mg/kg_mr39


title: WT IR-host_14

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_17


title: T cell normal control DP H3K27me3

tag: wbc

tag: fab subtype

tag: npm1 mutation


title: Panc-6.03 untreated, replica 3


title: T cell normal control CP H3K27me3

tag: chip antibody

tag: age

tag: status


title: WT IR-host_20

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_18


title: WT IR-host_12

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_16


title: T cell normal control BH H3K27me3

tag: flt3 mutation

tag: secondary?


title: WT IR-host_9

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_15


title: T cell normal control DP H3K9ac


title: T cell normal control BH H3K9ac


title: Panc-6.03 untreated, replica 1

tag: cell line

tag: cell type

tag: treated with


title: T cell normal control BK H3K27me3


title: Hs766T treated, replica 2

source_name: Hs766T treated


title: Hs766T treated, replica 3


title: WT IR-host_53

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_14

tag: tissue


title: T cell normal control BK H3K9ac


title: 150mg/kg_mr19

tag: mutation

tag: treatment


title: 150mg/kg_mr17


title: Hs766T untreated, replica 2

source_name: Hs766T untreated


title: 450mg/kg_mr31


title: WT IR-host_48

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_13

tag: strain

tag: host genotype/variation


title: 450mg/kg_mr32


title: WT IR-host_43

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_11


title: WT IR-host_44

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_12


title: 150mg/kg_mr18


title: Hs766T treated, replica 1


title: Hs766T untreated, replica 3


title: Hs766T untreated, replica 1


title: WT IR-host_39

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_9


title: WT IR-host_40

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_10


title: 150mg/kg_mr15


title: BxPC-3 treated, replica 3

source_name: BxPC-3 treated


title: 150mg/kg_mr14


title: 150mg/kg_mr16


title: Neutrophil normal control CP H3K27me3

source_name: Normal donor neutrophils

treatment_protocol: Neutrophils were obtained from the same normal donors as the T cells.  After the density gradient separation of the peripheral blood, the red cell containing pellet was lysed by resuspension in red cell lysis buffer (Prime) for a maximum of 20 minutes at room temperature.  Cells were washed in PBS containing 0.5% bovine serum albumin (Fisher Scientific) and 2mM EDTA.  Neutrophils were used immediately for subsequent ChIP or for RNA extraction without initial culture, as many cells degranulated and died during trial incubation periods.

tag: gender

tag: overall survival (months)

tag: karyotype


title: WT IR-host_36

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_8


title: WT IR-host_25

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_7


title: Neutrophil normal control JHR H3K27me3

tag: wbc

tag: fab subtype

tag: npm1 mutation


title: Neutrophil normal control JHR H3K9ac

tag: chip antibody

tag: age

tag: status


title: Neutrophil normal control DP H3K9ac

tag: flt3 mutation

tag: secondary?


title: Neutrophil normal control DP H3K27me3


title: BxPC-3 treated, replica 2

tag: cell line

tag: cell type

tag: treated with


title: WT IR-host_24

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_6

tag: tissue


title: Neutrophil normal control CP H3K9ac

description: Enrichment analysis of ChIP antibody-bound DNA vs input DNA


title: 150mg/kg_mr13

description:
TS603 R132H Glioma Xenograft Experiment 2
Gene Expression Data from xenografts

tag: mutation

tag: treatment


title: VEH_mr9

description:
TS603 R132H Glioma Xenograft Experiment 1
Gene Expression Data from xenografts

value: vehicle


title: BxPC-3 treated, replica 1


title: 150mg/kg_mr12


title: WT IR-host_22

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_5

tag: strain

tag: host genotype/variation


title: Neutrophil normal control BH H3K27me3

tag: gender

tag: overall survival (months)

tag: karyotype


title: BxPC-3 untreated, replica 3

source_name: BxPC-3 untreated


title: WT IR-host_16

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_3


title: WT IR-host_2

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_4


title: VEH_mr10


title: BxPC-3 untreated, replica 2


title: Neutrophil normal control BH H3K9ac

tag: wbc

tag: fab subtype

tag: npm1 mutation


title: VEH_mr6


title: Neutrophil normal control BK H3K9ac

tag: chip antibody

tag: age

tag: status


title: Panc-1 treated, replica 3

source_name: Panc-1 treated

tag: cell line


title: BxPC-3 untreated, replica 1

tag: cell type


title: VEH_mr5


title: WT IR-host_11

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_2


title: VEH_mr7


title: Neutrophil normal control BK H3K27me3

tag: flt3 mutation

tag: secondary?


title: Panc-1 treated, replica 2

tag: treated with


title: CD34 normal control 7 H3K27me3

source_name: Donor CD34+ HSCs

treatment_protocol: The CD34 positive fraction was obtained by magnetic bead separation according to the manufacturer’s protocol, using the CD34 MicroBead Kit (Miltenyi Biotech). Cells were frozen, thawed and cultured using the same conditions applied to AML patient samples.


title: CD34 normal control 5 H3K27me3


title: Panc-1 treated, replica 1


title: Panc-1 untreated, replica 2

source_name: Panc-1 untreated


title: VEH_mr4

tag: mutation

tag: treatment

tag: tissue


title: WT IR-host_10

description: mouse_p53null-mammary-tumor_wild-type_Irradiated host_sample_1

tag: strain

tag: host genotype/variation


title: WT Sham-IR-host_64

description: mouse_p53null-mammary-tumor_wild-type_sham-irradiated host_sample_8

source_name: Total RNA of p53null mammary tumor, WT-Sham-irradiated host

value: sham-irradiated wild-type


title: VEH_mr3


title: CD34 normal control 5 H3K9ac

tag: gender

tag: overall survival (months)

tag: karyotype


title: CD34 normal control 7 H3K9ac

tag: wbc

tag: fab subtype

tag: npm1 mutation


title: VEH_mr1


title: WT Sham-IR-host_61

description: mouse_p53null-mammary-tumor_wild-type_sham-irradiated host_sample_7


title: WT Sham-IR-host_65

description: mouse_p53null-mammary-tumor_wild-type_sham-irradiated host_sample_9


title: Panc-1 untreated, replica 3


title: IDH1i_980


title: VEH_995


title: WT Sham-IR-host_60

description: mouse_p53null-mammary-tumor_wild-type_sham-irradiated host_sample_6


title: CD34 normal control 3 H3K9ac

tag: chip antibody

tag: age

tag: status


title: CD34 normal control 4 H3K27me3

tag: flt3 mutation


title: CD34 normal control 4 H3K9ac

tag: secondary?


title: CD34 normal control 3 H3K27me3


title: Panc-1 untreated, replica 1

tag: cell line

tag: cell type

tag: treated with


title: normal human pancreatic ductal epthelial cells specimen 2, replica 3

value: normal human pancreatic ductal epithelial cells


title: VEH_965

tag: mutation

tag: treatment

tag: tissue


title: normal human pancreatic ductal epithelial cells specimen 1, replica 2


title: normal human pancreatic ductal epithelial cells specimen 1, replica 3


title: CD34 normal control 1 H3K9ac

tag: gender


title: normal human pancreatic ductal epthelial cells specimen 2, replica 2


title: WT Sham-IR-host_17

description: mouse_p53null-mammary-tumor_wild-type_sham-irradiated host_sample_3

tag: strain

tag: host genotype/variation


title: WT Sham-IR-host_8

description: mouse_p53null-mammary-tumor_wild-type_sham-irradiated host_sample_2


title: VEH_978


title: normal human pancreatic ductal epithelial cells specimen 1, replica 1


title: IDH1i_959


title: IDH1i_975


title: WT Sham-IR-host_3

description: mouse_p53null-mammary-tumor_wild-type_sham-irradiated host_sample_1


title: normal human pancreatic ductal epthelial cells specimen 2, replica 1


title: WT Sham-IR-host_46

description: mouse_p53null-mammary-tumor_wild-type_sham-irradiated host_sample_5


title: CD34 normal control 1 H3K27me3

tag: overall survival (months)

tag: karyotype

tag: wbc


title: VEH_962


title: Patient 26 H3K9ac

source_name: AML patient blasts

treatment_protocol: Cells were processed to obtain the mononuclear fraction by density gradient centrifugation using Histopaque (Sigma) and centrifugation at 1400 rpm at room temperature for 30 minutes. After washing in PBS containing 0.5% bovine serum albumin (Fisher scientific) and 2mM EDTA, cells were frozen in fetal calf serum (FCS) containing 10% DMSO (Sigma) and stored in liquid nitrogen.  Prior to use they were thawed and cultured at 37C, in a humidified atmosphere containing 5% CO2 in RPMI supplemented with 10% FCS and 2mMol L-glutamine for 24 hours.

tag: chip antibody

value: Female

tag: fab subtype

tag: npm1 mutation

value: no

value: ITD

value: NO


title: 6 = B7_KO_96h

city: Urbana

first: Yuechao

last: Zhao

state: IL

address: 407 S. Goodwin Ave

institute: University of Illinois

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G Plus.

data_processing: The data were analyzed with  GCOS2.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

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

growth_protocol: Human endometrial stromal cells were maintained in DMEM/F-12 medium containing 5% charcoal stripped fetal bovine serum

treatment_protocol: Independent hESC lines were established from individual biopsies of proliferative stage endometria, each cell line being from a different woman. These cultures were transfected with control (GL3 luciferase) or REA-specific siRNA for 24 h. siRNAs were then removed and cells were then treated for 24 h or 96 h in the presence of the hormone cocktail containing 10 nM E2, 1 µM progesterone and 0.5 µM 8Br-cAMP (E+P+cAMP). Cells were harvested and total RNA was prepared with TRIzol reagent. RNA integrity was verified using an Agilent 2100 Bioanalyser.

value: primary cultured human endometrial stromal cells (hESCs)

tag: transfected with

value: REA-specific siRNA for 24 h

value: [E2+P4+cAMP] hormone cocktail for 96hr


title: IDH1i_942


title: Patient 25 H3K9ac

value: Male

tag: age

tag: status

tag: flt3 mutation

tag: secondary?


title: Patient 24 H3K9ac

value: DD


title: VEH_801

tag: mutation


title: Patient 23 H3K9ac

value: TKD


title: IDH1i_808

tag: treatment


title: Z138-shSOX11.3

city: Barcelona

first: Virginia

last: Amador

address: Rossello 153

country: Spain

institute: IDIBAPS

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HU133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the 7G- 3000.

data_processing: The data were analyzed with the Expression Console application from Affymetrix. We performed MAS5.0 to summarize the data.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using the 3' IVT Express kit from Affymetrix.

extract_protocol: Total RNA was extracted from the Z138 MCL cell line stable lentivirally transduced with different shRNA constructs specifically targeting SOX11 (shSOX11.1 and shSOX11.3), and two scramble shRNA constructs (shControl.1 and shControl.2) using TRIZOL. RNA quality and quantity were assessed using the Bioanalyzer 2100 and Nanodrop spectrophotometer.

tag: cell line

tag: cell type

value: mantle cell lymphoma (MCL) cells

tag: shRNA


title: Z138-shSOX11.1


title: 4 = N16_KO_24h

tag: treated with

value: [E2+P4+cAMP] hormone cocktail for 24hr


title: Patient 22 H3K9ac

value: H3K9ac (recognizes H3K9/K14 Acetylation):Millipore 06-599 lot# JBC1349702

tag: gender

tag: overall survival (months)

value: yes

value: Input DNA


title: Patient 21 H3K9ac

tag: karyotype

tag: wbc


title: 7 = N16_siGL3_96h

value: control (GL3 luciferase) for 24 h


title: 8 = N16_KO_96h


title: 5 = B7_siGL3_96h


title: Patient 20 H3K9ac

tag: chip antibody

value: AL

value: add 11 (p15) in 6/20 chromosomes

tag: fab subtype


title: 3 = N16_siGL3_24h

tag: transfected with


title: IgG, 2.5-6h

type: SRA

first: Jakub

middle: Orzechowski

last: Westholm

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan-Kettering Cancer Center

library_source: genomic

data_processing:
Mapping to the Drosophila dm3 genome, using Bowtie, parameters –v 2 –m 1, (i.e. allowing 2 mismatches and only using uniquely mapping reads)
Peak calling using Quest, comparing Insv ChIP to IgG control for each time point. The following parameters were used: bandwidth = 30, region size = 300 ChIP enrichment = 10, ChIP to background enrichment = 2.5, ChIP extension enrichment = 3
Genome_build: dm3
Supplementary_files_format_and_content: 2 bed files with Insv peaks, one for 2.5-6h and one for 6.5-12h.

source_name: w[1118]  embryos

growth_protocol: embryos were aged and collected at 25 degrees

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: genotype

tag: developmental stage

value: IgG


title: IgG, 6.5-12h


title: Insv ChIP, 6.5-12h

value: Insensitive


title: 2 = B7_KO_24h


title: wt rep3

hyb_protocol: standand for Drosophila gene ChIP 2.0 (done at the Genomic Core Laboratory at Memorial Sloan-Kettering Cancer Center)

data_processing: R/Bioconductor GCRMA

source_name: embryos 6-8h

growth_protocol: wt and insv flies were grown at 25 degrees before collecting embryos from. Embryos were aged under the same temperature.

extract_protocol: Trizol reagent from Invitrogen


title: WT Sham-IR-host_31

description: mouse_p53null-mammary-tumor_wild-type_sham-irradiated host_sample_4

tag: strain

value: BALB/c

tag: tissue

value: transplanted p53null mammary tumor

tag: host genotype/variation

value: sham-irradiated wild-type


title: Z138-shControl.1


title: Insv ChIP, 2.5-6h


title: wt rep2

scan_protocol: standand for Drosophila gene ChIP 2.0 (done at the Genomic Core Laboratory at Memorial Sloan-Kettering Cancer Center)


title: insensitive rep3

label_protocol: standand for Drosophila gene ChIP 2.0 (done at the Genomic Core Laboratory at Memorial Sloan-Kettering Cancer Center)

value: Insensitive mutant, insv[23B]


title: Z138-shControl.2


title: 1 = B7_siGL3_24h

value: primary cultured human endometrial stromal cells (hESCs)


title: Patient 17 H3K9ac

description: Enrichment analysis of ChIP antibody-bound DNA vs input DNA

value: Female

tag: age

tag: status

tag: npm1 mutation

tag: flt3 mutation

value: no

tag: secondary?

value: NO


title: Patient 19 H3K9ac

tag: gender

value: Male


title: wt rep1


title: insensitive rep2


title: miRNA expression in fertilized embryonic stem cells, rep 3

description:
Sample 8
small RNA
Fertilized embryonic stem cell (fESC, FE).

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Mouse v2 MicroRNA expression BeadChip according to the protocols provided by the manufacturer.

source_name: Mouse fertilized embryonic stem cell (fESC)

label_protocol: Biotinylated cDNA were prepared from 0.2-1ug total RNA. The miRNA method targets specific sequences with sets of oligonucleotides that are extended and labeled during PCR amplification.

value: female and male

tag: cell type

value: fertilized embryonic stem cells

tag: chromosomes contained

value: both X and Y

tag: passage


title: miRNA expression in fertilized embryonic stem cells, rep 1

description:
Sample 6
small RNA
Fertilized embryonic stem cell (fESC, FE).


title: miRNA expression in fertilized embryonic stem cells, rep 2

description:
Sample 7
small RNA
Fertilized embryonic stem cell (fESC, FE).


title: miRNA expression in parthenogenetic embryonic stem cells, rep 2

description:
Sample 5
small RNA
Parthenogenetic embryonic stem cell (pESC, PA).

source_name: Mouse parthenogenetic embryonic stem cell (pESC)

value: female

value: parthenogenetic embryonic stem cells


title: Patient 18 H3K9ac

tag: chip antibody

value: H3K9ac (recognizes H3K9/K14 Acetylation):Millipore 06-599 lot# JBC1349702

value: DD

tag: overall survival (months)

tag: karyotype

tag: wbc

value: yes

value: ITD

value: Input DNA


title: p65 KO mouse KLSF #2

city: Chapel Hill

first: Sarah

last: Stein

state: NC

address: 450 West Dr.

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: SAMPLE 5

hyb_protocol: Samples were hybridized to Affymetrix Mouse Gene Chip 1.0 ST arrays and scanned at the UNC Affymetrix Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing:
RMA expression value derived from Expression Console software, and analysis was performed using Partek Genomics Suite.
affymetrix-algorithm-name = rma-gene-default, affymetrix-algorithm-version = 1.0, program-name = Expression Console, program-version = 1.1.2800.28061

source_name: p65 KO_KLSF

label_protocol: RNA was amplified and labeled using the Nugen Ovation Pico WTA System V2.

growth_protocol: Murine bone marrow lineage-Flk2-Sca-1+c-kit+ cells were sorted directly into buffer RLT (Qiagen) with 1% β-Mercaptoethanol.

extract_protocol: RNA was extracted with the RNEasy Mini Kit (Qiagen).

tag: genotype/variation

value: p65 knockout

value: bone marrow lineage-Flk2-c-kit+Sca-1+ cells


title: Patient 15 H3K9ac

tag: fab subtype


title: Patient 13 H3K9ac

value: AL


title: p65 WT mouse KLSF #3

description: SAMPLE 3

source_name: p65 WT_KLSF

value: p65 wild-type


title: Patient 14 H3K9ac

value: monosomy 7

value: no


title: Patient 12 H3K9ac

value: Female

value: NO


title: p65 WT mouse KLSF #2

description: SAMPLE 2


title: p65 KO mouse KLSF #1

description: SAMPLE 4


title: miRNA expression in androgenetic embryonic stem cells, rep 3

description:
Sample 3
small RNA
Androgenetic embryonic stem cell: aESC (AN).

source_name: Mouse androgenetic embryonic stem cell (aESC)

tag: strain

value: female and male

value: androgenetic embryonic stem cells


title: miRNA expression in parthenogenetic embryonic stem cells, rep 1

description:
Sample 4
small RNA
Parthenogenetic embryonic stem cell (pESC, PA).

value: female


title: Patient 16 H3K9ac

value: Male


title: miRNA expression in androgenetic embryonic stem cells, rep 2

description:
Sample 2
small RNA
Androgenetic embryonic stem cell: aESC (AN).

value: both X and Y


title: Patient 11 H3K9ac

value: H3K9ac (recognizes H3K9/K14 Acetylation):Millipore 06-599 lot# JBC1349702


title: p65 KO mouse KLSF #3

description: SAMPLE 6


title: Patient 8 H3K9ac

value: abnormal chrom 3 (?q26) + marker


title: p65 WT mouse KLSF #1

description: SAMPLE 1


title: Patient 9 H3K9ac


title: insensitive rep1

tag: genotype

value: Insensitive mutant, insv[23B]


title: EWS-ATF1_48h_control

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: RNeasy Plus Mini kit

tag: strain background

value: mixed background of C57/BL6, 129, and ICR

value: tumor cells


title: EWS-ATF1_tumor1

description: 1281 mune tumor1_(MoGene-1_0-st-v1)

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials: Heat cocktails at 99C for 5 minutes, then 45Cfor 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP), Transfer 80μl of hyb solution to each array, then tape holes and parafilm, Hybridize 17 hours at 45C at 60rpm, Fluidics washing is FS450_0007.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 TG

data_processing: Data were quantile normalized using Genespring GX software. Control probes are automatically excluded by Genespring software resulting 28,856 probes, which are associated with gene expressions.

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

tag: tissue origin

value: soft tissue sarcoma


title: EWS-ATF1_48h_highDox


title: Patient 6 H3K9ac

tag: age

tag: status

value: AL

value: CML blast crisis

tag: npm1 mutation

value: YES

value: Input DNA


title: EWS-ATF1_3h_lowDox


title: EWS-ATF1_24h_highDox

description: 1297 Doxoff Dox0.2 24h_(MoGene-1_0-st-v1)


title: miRNA expression in androgenetic embryonic stem cells, rep 1

description:
Sample 1
small RNA
Androgenetic embryonic stem cell: aESC (AN).

tag: gender


title: Patient 10 H3K9ac

value: yes

tag: flt3 mutation

value: TKD

tag: secondary?


title: EWS-ATF1_3h_highDox

tag: cell type


title: Patient 7 H3K9ac

tag: chip antibody

value: Female

value: DD

value: ITD

value: NO


title: Patient 5 H3K9ac

value: Male

tag: overall survival (months)

value: inv 16

value: no


title: Patient 4 H3K9ac

value: H3K9ac (recognizes H3K9/K14 Acetylation):Millipore 06-599 lot# JBC1349702

tag: karyotype


title: EWS-ATF1_3h_control

value: mixed background of C57/BL6, 129, and ICR


title: EWS-ATF1_control

description: 1297 Doxoff_(MoGene-1_0-st-v1)

value: tumor cells


title: Patient 3 H3K9ac

tag: wbc


title: Patient 1 H3K9ac


title: Patient 2 H3K9ac


title: 18q-119c

status: Public on Apr 03 2013

city: Atlanta

first: Karen

middle: E

last: Hermetz

state: GA

address: 1518 Clifton Rd

department: Human Genetics

institute: Emory University School of Medicine

hyb_protocol: Labeled DNA and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on a GenePix 4000B scanner or an Agilent high-resolution C scanner.

data_processing: Signal intensities were evalutated using Feature Extraction software (log ratios from Feature Extraction files included in Sample tables) and Genomic Workbench was used to analyze array data and make breakpoint predictions (Genomic Workbench data and README file provided as supplementary files on the Series record).

source_name: patient genomic DNA

label_protocol: Genomic DNA, 0.5-1ug, from patient samples and controls were Cy3/Cy5 labeled with Agilent Genomic DNA Enzymatic Labeling Kit following manufacture's protocol

extract_protocol: Genomic DNA was extracted from peripheral blood or cell lines using Gentra Puregene DNA Extraction kit following manufacturers protocol

value: F

tag: array number

tag: chromosome affected

tag: cnv type

value: duplication adjacent to terminal deletion

source_name: Normal control DNA

value: M

tag: cell line


title: WT CD8 T, steady-state, replicate 1

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

description:
Sample name: C28
WT spleen CD8 T lymphocytes from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marrow chimera mice, FACS sorted as: live, CD3(pos), CD8a(pos)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430.2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v5 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were MAS5.0 normalized in R and Bioconductor using the affy package.

label_protocol: 35 to 50 ng of RNA from each sample were used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from between 5x10E4 and 3x10E6 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, with on-column DNase digestion, according to the manufacturer protocol.

treatment_protocol: Mice were infected intraperitoneally with salivary gland-murine cytomegalovirus (5x10e4 pfu/mouse). Spleens were harvested at 36 hours post-infection and digested with collagenase (Liberase CI), erythrocytes were lysed with NH(4)Cl, and leukocytes were resuspended in PBS EDTA 5mM before sorting by flow cytometry.

tag: strain

tag: chimera description

tag: genotype/variation

value: WT

value: CD8 T lymphocytes

tag: infection


title: WT CD8 T, steady-state, replicate 2

description:
Sample name: B22
WT spleen CD8 T lymphocytes from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marrow chimera mice, FACS sorted as: live, CD3(pos), CD8a(pos)


title: 18q-65c


title: WT B, MCMV, replicate 2

description:
Sample name: A11
WT spleen B lymphocytes from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marrow chimera mice, FACS sorted as: live, CD19(pos)

value: B lymphocytes

value: MCMV


title: 18q-186c


title: WT CD8 T, MCMV, replicate 1

description:
Sample name: A5
WT spleen CD8 T lymphocytes from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marrow chimera mice, FACS sorted as: live, CD3(pos), CD8a(pos)


title: WT B, MCMV, replicate 1

description:
Sample name: B18
WT spleen B lymphocytes from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marrow chimera mice, FACS sorted as: live, CD19(pos)


title: 18q-139c


title: WT CD8 T, MCMV, replicate 2

description:
Sample name: C38
WT spleen CD8 T lymphocytes from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marrow chimera mice, FACS sorted as: live, CD3(pos), CD8a(pos)


title: WT B, steady-state, replicate 2

description:
Sample name: C34
WT spleen B lymphocytes from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marrow chimera mice, FACS sorted as: live, CD19(pos)


title: SG_Tel_009


title: 18q-62c


title: 18q-26c


title: 18q-34c


title: WT CD11b DC, MCMV, replicate 2b

description:
Sample name: MDD_B26
WT spleen CD11b+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.1(pos)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430.2 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v5 protocol.

label_protocol: Except for sample A7 where only 8 ng was available, 50 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from between 5x10E4 and 3x10E6 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.

treatment_protocol: Mice were infected intraperitoneally with salivary gland-murine cytomegalovirus (5x10e4 pfu/mouse). Spleens were harvested at 36 hours post-infection and digested with collagenase (Liberase CI), erythrocytes were lysed with NH(4)Cl, and leukocytes were resuspended in PBS EDTA 5mM before sorting by flow cytometry

value: CD11b+ dendritic cells (DC)

value: murine cytomegalovirus


title: EGL010


title: SG_Tel_003


title: WT B, steady-state, replicate 1

description:
Sample name: A1
WT spleen B lymphocytes from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marrow chimera mice, FACS sorted as: live, CD19(pos)


title: SG_Tel_020


title: EGL044


title: SG_Tel_008


title: IFNAR-/- CD11b DC, MCMV, replicate 2b

description:
Sample name: MDD_C39
IFNAR-KO spleen CD11b+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.2(pos)

value: IFNAR-KO


title: SG_Tel_022


title: IFNAR-/- CD8a DC, steady-state, replicate 2b

description:
Sample name: MDD_A10
IFNAR-KO spleen CD8a+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.2(pos)

value: CD8a+ dendritic cells (DC)


title: WT NK, steady-state, replicate 2b

description:
Sample name: MDD_B24
WT spleen natural killer (NK) cells from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.1(pos)

value: natural killer (NK) cells


title: SG_Tel_019


title: EGL074


title: SG_Tel_018


title: IFNAR-/- CD11b DC, steady-state, replicate 1b

description:
Sample name: MDD_C29
IFNAR-KO spleen CD11b+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.2(pos)


title: WT NK, MCMV, replicate 2b

description:
Sample name: MDD_C40
WT spleen natural killer (NK) cells from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.1(pos)


title: IFNAR-/- CD11b DC, steady-state, replicate 2b

description:
Sample name: MDD_B23
IFNAR-KO spleen CD11b+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.2(pos)


title: WT CD8a DC, MCMV, replicate 1b

description:
Sample name: MDD_B20
WT spleen CD8a+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.1(pos)


title: SMM8

city: Bronx

first: Christoph

last: Heuck

address: 1300 Morris Park Ave

department: Cancer Center

institute: Albert Einstein College of Medicine

description:
LMM10029A
Methylation data from HELP assay

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background.PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.)

source_name: SMM_CD138+ selected cells

label_protocol: Random 9-mers pre-labeled with either Cy5 or Cy3

extract_protocol: Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). Total More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers.Genomic DNA was isolated using Puregene Cell and Tissue Kit according to the manufacturer instructions (Qiagene).  Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol  Khulan B et al. Genome Res. 2006 Aug;16(8):1046-55).

tag: subject condition

value: smoldering myeloma

value: CD138+ selected cells from bone marrow aspirates

tag: restriction enzyme used

value: MspI

tag: gdna digeted with

value: HpaII


title: MGUS8

description:
LMM10035
Methylation data from HELP assay

source_name: MGUS_CD138+ selected cells

value: monoclonal gammopathy of uncertain significance


title: MGUS10

description:
LMM10045A
Methylation data from HELP assay


title: MGUS9

description:
LMM10040A
Methylation data from HELP assay


title: SG_Tel_005_sib

tag: gender

value: F


title: WT CD8a DC, steady-state, replicate 1b

description:
Sample name: MDD_A3
WT spleen CD8a+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.1(pos)

tag: cell type


title: IFNAR-/- CD11b DC, MCMV, replicate 1b

description:
Sample name: MDD_A6
IFNAR-KO spleen CD11b+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.2(pos)


title: WT CD11b DC, MCMV, replicate 1b

description:
Sample name: MDD_C32
WT spleen CD11b+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.1(pos)


title: EGL398

value: duplication adjacent to terminal deletion


title: WT CD8a DC, steady-state, replicate 2b

description:
Sample name: MDD_C36
WT spleen CD8a+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.1(pos)


title: WT CD11b DC, steady-state, replicate 1b

description:
Sample name: MDD_B16
WT spleen CD11b+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.1(pos)


title: IFNAR-/- CD8a DC, MCMV, replicate 1b

description:
Sample name: MDD_C33
IFNAR-KO spleen CD8a+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.2(pos)


title: SG_Tel_004

value: M


title: SG_Tel_023


title: IFNAR-/- CD8a DC, steady-state, replicate 1b

description:
Sample name: MDD_B17
IFNAR-KO spleen CD8a+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.2(pos)


title: SG_Tel_024


title: REL1

description:
LMM06020B
Methylation data from HELP assay

source_name: REL_CD138+ selected cells

value: relapsed myeloma


title: WT CD11b DC, steady-state, replicate 2b

description:
Sample name: MDD_A9
WT spleen CD11b+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.1(pos)

value: WT


title: SG_Tel_006_sib


title: WT NK, MCMV, replicate 1b

description:
Sample name: MDD_A7
WT spleen natural killer (NK) cells from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.1(pos)


title: WT NK, steady-state, replicate 1b

description:
Sample name: MDD_C30
WT spleen natural killer (NK) cells from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.1(pos)


title: SG_Tel_016


title: MLL-AF6 leukemia Z237 BM Replicate 3 of 3

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
Sacrificed terminally ill leukemic mouse
Gene expression data from a MLL-AF6 positive murine leukemic marrow

hyb_protocol: According to manufacturer's instructions (Affymetrix)

data_processing: RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).

source_name: Whole bone marrow cells from a retroviral mouse model of MLL-AF6

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA and Qiagen RNeasy micro kit was performed according to the manufacturer's instructions.

treatment_protocol: Cells were not subject to any treatment prior to RNA preparation.

value: bone marrow leukemic cells

tag: disease state

value: MLL-AF6 leukemia


title: MGUS1

description:
LMM06007B
Methylation data from HELP assay


title: KAP1 WT CD71+Ter119+ sorted cells_C6

city: Lausanne

first: Adamandia

last: Kapopoulou

address: Station 15

department: Sciences de la Vie

country: Switzerland

institute: EPFL

description:
C6
sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP

hyb_protocol: Hybridization on Mouse WG 6 v2 expression arrays (Illumina) was carried out according to the manufacturer’s instructions

scan_protocol: Scanning was carried out according to the manufacturer’s instructions

data_processing:
Data were normalized and analyzed using Illumina Beadstudio 3.1.3 (background correction and quantile normalization).
Expression profiles of each sample were imported into GeneSpringGX 7.3.1 (Agilent Technologies, USA).
In addition to expression values, Illumina BeadStudio software computes a detection p-value. Based on this, each probe was assigned a detection flag (P (present): p < 0.045; M (Marginal): p between 0.050 and 0.045, A (Absent): p>0.05). Expression values below a defined threshold (i.e. 20) are set to the threshold in order to remove negative values after background correction. To identify dysregulated genes in KO mice, t-test and/or ANOVA and additional steps of filtering were carried out

source_name: KAP1 WT CD71+Ter119+ sorted cells

label_protocol: 100 ng of RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion

growth_protocol: no

extract_protocol: Ter119+CD71+ mouse cells were sorted by flow cytometry RNA was extracted by TriZol, following manufacturer instructions

treatment_protocol: no

value: mix strain

tag: tissue

value: bone marrow

value: CD71+Ter119+ cells (sorted)

tag: age

value: 8- to 12-wk-old

value: KAP1 WT


title: NEWMM4

description:
LMM06056B1
Methylation data from HELP assay

source_name: NEWMM_CD138+ selected cells

value: newly diagnosed myeloma


title: MGUS3

description:
LMM06024B
Methylation data from HELP assay

value: CD138+ selected cells from bone marrow aspirates


title: MLL-AF6 leukemia Z236 BM Replicate 2 of 3

scan_protocol: According to manufacturer's instructions (Affymetrix)


title: KAP1 WT CD71+Ter119+ sorted cells_C8

description:
C8
sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP


title: MGUS2

description:
LMM06019B
Methylation data from HELP assay

value: MspI


title: KAP1 WT CD71+Ter119+ sorted cells_C9

description:
C9
sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP


title: KAP1 WT CD71+Ter119+ sorted cells_C4

description:
C4
sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP


title: MLL-AF6 leukemia Z233 BM Replicate 1 of 3


title: KAP1 KO CD71+Ter119+ sorted cells_A13+

description:
A13+
sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP

source_name: KAP1 KO CD71+Ter119+ sorted cells

value: KAP1 KO


title: NL5

description:
CD138E
Methylation data from HELP assay

source_name: NL_CD138+ selected cells

value: normal donor

value: HpaII


title: KAP1 KO CD71+Ter119+ sorted cells_A11+

description:
A11+
sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP


title: SG_Tel_007

value: F

value: duplication adjacent to terminal deletion


title: MGUS11

description:
LMM09086
Methylation data from HELP assay

value: monoclonal gammopathy of uncertain significance


title: MGUS4

description:
LMM06025B
Methylation data from HELP assay


title: M397

value: M


title: 18q-105c


title: MGUS7

description:
LMM09083C
Methylation data from HELP assay


title: 18q-107c


title: MGUS5

description:
LMM06026B
Methylation data from HELP assay


title: REL8

description:
LMM06058B2
Methylation data from HELP assay

value: relapsed myeloma


title: KAP1 KO CD71+Ter119+ sorted cells_A4+

description:
A4+
sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP


title: REL3

description:
LMM06051B2
Methylation data from HELP assay


title: NEWMM1

description:
LMM06013B1
Methylation data from HELP assay


title: IFNAR-/- CD8a DC, MCMV, replicate 2b

description:
Sample name: MDD_B27
IFNAR-KO spleen CD8a+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.2(pos)

value: IFNAR-KO

value: CD8a+ dendritic cells (DC)

value: murine cytomegalovirus


title: NL6

description:
CD138F
Methylation data from HELP assay


title: M396


title: HT1080_dsRNA-treated_rep1

city: Cleveland

first: Ganes

middle: C.

last: Sen

address: 9500 Euclid Avenue NE-20

institute: Cleveland Clinic

description: HT+

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI

label_protocol: biotinylated cRNAs prepared using Ambion’s Illumina TotalPrep-96 RNA Amplification kit

extract_protocol: RNA was extracted with Trizol reagent, followed DNase I treatment and clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: fibrosarcoma cells

tag: treated with

value: 100 ug/ml dsRNA (polyIC) for 6h


title: WT CD8a DC, MCMV, replicate 2b

description:
Sample name: MDD_A13
WT spleen CD8a+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(pos), CD45.1(pos)

value: WT


title: NEWMM2

description:
LMM06021B1
Methylation data from HELP assay

value: newly diagnosed myeloma


title: PKC_inhibitor-treated_HT1080_dsRNA-treated_rep1

tag: pre-treated with

value: Go6976 (5uM) for 1hr


title: HT1080_untreated_rep1

description: HT-

source_name: HT1080_untreated control


title: PKC_inhibitor-treated_HT1080_untreated_rep1


title: REL14

description:
LMM09015C
Methylation data from HELP assay

value: CD138+ selected cells from bone marrow aspirates

value: MspI


title: SMM1

description:
LMM06040B2
Methylation data from HELP assay

value: smoldering myeloma


title: embryo injected with anti-mir-34LNA, kept for 24hpf, biological rep3

city: NEW DELHI

first: Kartik

last: Soni

address: Mathura Road

department: FGU

country: India

institute: INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY

description: Gene expression data from Zebrafish embryos at 24 hour post fertilization(hpf) indicating zygotic set of transcripts

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Initial QC and processing was done using Affymetrix GeneChip Operating Software(GCOS) to obtain the raw signal intensities. The data were analyzed with Avadis using the default analysis settings and quantile normalization as normalization method afer being log transformed.

organism: Danio rerio

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

growth_protocol: 1-2 cell stage embryos were collected for microinjection. Following injections the embryos were  aged at 30C and were lated collected at the different time points (1hpf, 7hpf and 24hpf)

extract_protocol: Total RNA was extracted using Trizol as per the manufacturer's instructions.

treatment_protocol: Embryos were collected at one cell stage. Embryos were injected with anti-mir-34LNA of mockLNA at the 1-2 cell stage and were harvetyes at the specified time points of 1hpf, 7hpf and 24hpf. The embryos were also monitoredunder the dissecting microscope for any developmental abnormalities of phenotypic defects. Selected embryos were transferred to a fresh petriplate. The injected embryos at 7hpf and 24hpf were dechorionated manually, rinsed with distilled water and placed on ice in the Trizol solution (GibcoBRL).

tag: genotype

value: wild type

value: anti-mir-34LNA injected embryos, dechorionated

tag: embryo age

value: 24 hour post fertilization


title: NEWMM3

description:
LMM06049B2
Methylation data from HELP assay

value: HpaII


title: NL8

description:
CD138H
Methylation data from HELP assay

value: normal donor


title: embryo injected with anti-mir-34LNA, kept for 24hpf, biological rep1


title: REL2

description:
LMM06034B1
Methylation data from HELP assay

value: relapsed myeloma


title: NL7

description:
CD138G
Methylation data from HELP assay


title: KAP1 KO CD71+Ter119+ sorted cells_A8+

description:
A8+
sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP

value: mix strain

value: bone marrow

value: CD71+Ter119+ cells (sorted)

value: 8- to 12-wk-old

value: KAP1 KO


title: SG_Tel_026

value: F

tag: array number

tag: chromosome affected

tag: cnv type

value: duplication adjacent to terminal deletion

value: M

tag: cell line


title: REL6

description:
LMM09005A
Methylation data from HELP assay

value: CD138+ selected cells from bone marrow aspirates


title: embryo injected with anti-mir-34LNA, kept for 24hpf, biological rep2


title: REL7

description:
LMM06035B
Methylation data from HELP assay

value: MspI


title: REL5

description:
LMM08091B
Methylation data from HELP assay


title: embryo injected with anti-mir-34LNA, kept for 7hpf, biological rep2

description: Gene expression data from Zebrafish embryos at 7 hour post fertilization(hpf) indicating transcript pool during maternal to zygotic transcription

value: 7 hour post fertilization


title: embryo injected with anti-mir-34LNA, kept for 7hpf, biological rep3

value: wild type


title: embryo injected with mockLNA, kept for 24hpf, biological rep1

value: mockLNA injected embryos, dechorionated


title: embryo injected with mockLNA, kept for 24hpf, biological rep3

value: 24 hour post fertilization


title: embryo injected with anti-mir-34LNA, kept for 7hpf, biological rep1

value: anti-mir-34LNA injected embryos, dechorionated


title: REM1

description:
LMM08089B
Methylation data from HELP assay

source_name: REM_CD138+ selected cells

value: clinical complete remission

value: HpaII


title: embryo injected with mockLNA, kept for 7hpf, biological rep3


title: embryo injected with mockLNA, kept for 24hpf, biological rep2


title: embryo injected with mockLNA, kept for 7hpf, biological rep2


title: embryo injected with mockLNA, kept for 7hpf, biological rep1


title: REL18

description:
LMM09026A
Methylation data from HELP assay

value: relapsed myeloma


title: REL17

description:
LMM09024A
Methylation data from HELP assay


title: embryo injected with mockLNA, kept for 1hpf, biological rep3

description: Gene expression data from Zebrafish embryos at 1 hour post fertilization(hpf) indicating maternal set of transcripts

value: mockLNA injected embryos

value: 1 hour post fertilization


title: REL15

description:
LMM09020B
Methylation data from HELP assay


title: REL16

description:
LMM09021A
Methylation data from HELP assay


title: MGUS6

description:
LMM09017A
Methylation data from HELP assay

value: monoclonal gammopathy of uncertain significance


title: REL13

description:
LMM09012B
Methylation data from HELP assay


title: embryo injected with anti-mir-34LNA, kept for 1hpf, biological rep2

value: anti-mir-34LNA injected embryos


title: embryo injected with mockLNA, kept for 1hpf, biological rep2


title: NEWMM10

description:
LMM08081A
Methylation data from HELP assay

value: newly diagnosed myeloma


title: embryo injected with anti-mir-34LNA, kept for 1hpf, biological rep1


title: embryo injected with anti-mir-34LNA, kept for 1hpf, biological rep3


title: REL12

description:
LMM09006B
Methylation data from HELP assay


title: NEWMM9

description:
LMM08068D
Methylation data from HELP assay


title: low R/FR_SA spray, biological rep 3

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

department: Plant Ecophysiology

country: Netherlands

institute: Utrecht University

hyb_protocol: The (#900720) GeneChip Hybridization, Wash and Stain Kit was used for hybridization, washing, staining and scanning of the chips.

scan_protocol: The software program Affymetrix 'GeneChip Command Console (v3.1)' was used to operate the staning, washing and scanning of the GeneChips and visual inspection of the array images. Chips were scanned using the Affymetrix 3000G scanner

data_processing: Data were processed using the Bioconductor packages in R and using the RMA normalization algorithm.

organism: Arabidopsis thaliana

source_name: Arabidopsis petioles, 2h low R/FR + SA treatment

label_protocol: The Affymetrix 3'IVT-Express Labeling Kit was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labelling reactions.

growth_protocol: Arabidopsis thaliana plants were sown, stratified (4˚C) for 3 days and then transferred to a growth chamber (9 h. light (180 µmol / m2 / s, 20°C, 70% RH, R/FR = 2.2), 15 h dark) where they were transferred to individual pots after 10 d and gwon until 4 weeks old.

extract_protocol: Total RNA was isolated from homogenized material using the RNeasy plant mini kit (Qiagen) with on-column DNA digestion following the company’s instructions

treatment_protocol: Plants were put in each of the four conditions (control light with mock spray, control light with 0.5 mM SA spray, low R:FR (0.2) with mock spray, low R:FR (0.2) with 0.5 mM SA spray) for 2h. One petiole (approx. 5 mm length) per plant was harvested in liquid N2. 3 petioles/biological replicate were pooled.

tag: organ

value: petiole

value: 4 weeks old

tag: treatment

value: low R/FR, SA spray


title: REL11

description:
LMM08066B
Methylation data from HELP assay

tag: subject condition

value: CD138+ selected cells from bone marrow aspirates

tag: restriction enzyme used

value: MspI


title: NEWMM12

description:
LMM08059D
Methylation data from HELP assay

tag: gdna digeted with


title: REM2

description:
LMM08082D
Methylation data from HELP assay

tag: cell type


title: SMM6

description:
LMM08075B
Methylation data from HELP assay

value: smoldering myeloma


title: low R/FR_SA spray, biological rep 1


title: SG_Tel_010

tag: gender

value: F

value: duplication adjacent to terminal deletion

value: M


title: SG_Tel_015


title: low R/FR_SA spray, biological rep 2


title: EGL399


title: embryo injected with mockLNA, kept for 1hpf, biological rep1

value: wild type

tag: tissue


title: low R/FR_mock spray, biological rep 1

source_name: Arabidopsis petioles, 2h low R/FR treatment

tag: age

value: low R/FR, mock spray


title: low R/FR_mock spray, biological rep 2


title: EGL106


title: EGL104


title: EGL099


title: NEWMM8

description:
LMM08056C
Methylation data from HELP assay

value: HpaII


title: 18q-233c


title: NEWMM5

description:
LMM08047
Methylation data from HELP assay


title: NEWMM7

description:
LMM08053A
Methylation data from HELP assay


title: high R/FR_SA spray, biological rep 3

source_name: Arabidopsis petioles, 2h SA treatment

value: high R/FR (control), SA spray


title: high R/FR_SA spray, biological rep 2


title: A549, H3N2, 24hpi (rep3)

city: Lyon

first: olivier

last: Terrier

address: Rue Guillaume Paradin

department: Laboratoire de Virologie et Pathologie Humaine

institute: Université Claude Bernard Lyon 1

description:
Human influenza-infected cells
Sample name: H3C

data_processing:
For each miRNA, the expression level was determined by the 2(-Delta Delta C(T)) method (Livak & Schmittgen, 2001). Data were normalized using the small nucleolar human RNA RNU48 as a control.
1st step of normalization: CT correction based on the global mean CT obtained between plates
2nd step of normalization: Target gene signal normalized to housekeeping gene RNU48

label: FAM

source_name: A549 cells (ATCC  number CCL-185)

label_protocol: Reverse transcription reactions contained 390 ng of purified RNAs, 1x Megaplex RT primers (Human pool A v2.1, Applied Biosystems), 1x RT buffer, 2.5 mM of each dNTP, 3 mM MgCl2, 1U/µL of Multiscribe reverse transcriptase (Applied Biosystems) and 0.3 U/µL of RNase inhibitor (Applied Biosystems). The RT reaction had a final volume of 7.5 µL and was incubated for 5 min on ice, followed by 40 cycles (16°C 2 min, 42°C 1 min, 50°C 1 sec), 85°C 5 min and then held at 4°C. The RT products were subsequently amplified with sequence-specific primers contained in a TaqMan array MicroRNA card (card A, Applied Biosystems), which enables the simultaneous quantification of 377 different human miRNAs plus several endogenous controls. Six µL of RT products were diluted in 444 µL of nuclease-free water and mixed with 450 µL of 2x TaqMan Universal PCR Master Mix with no Amperase (Applied Biosystems) and dispensed into the 384 wells by centrifugation. The plates were incubated at 95°C for 10 min, followed by 40 cycles (95°C 15 sec, 60°C 1 min). The data were collected and processed using the Plate Utility and Automation Controller software (Applied Biosystems).

growth_protocol: Confluent A549 cells were Mock-infected or infected with influenza viruses at an MOI of 1 or 10-3 for 1 h in a minimal volume of DMEM supplemented with 2 mM L-glutamine, 100 U/mL of penicillin, 100 µg/mL of streptomycin sulphate and 0.5 µg/mL of trypsin (infection medium) at 37°C. The cells were then overlaid with fresh infection medium and incubated at 37°C for 24 h.

extract_protocol: Total RNAs, including small RNAs, were isolated using Qiazol reagent (Qiagen) in combination with the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol. Purified RNAs were eluted in 30µL RNase-free water.

value: A549 cells (ATCC  number CCL-185)

tag: infection


title: NEWMM6

description:
LMM08052D
Methylation data from HELP assay


title: REL4

description:
LMM08058A
Methylation data from HELP assay

value: relapsed myeloma


title: A549, H3N2, 24hpi (rep2)

description:
Human influenza-infected cells
Sample name: H3B


title: SMM2

description:
LMM08049
Methylation data from HELP assay


title: S.cerevisiae genes : wild type  vs. KDX1 over-expressed cells

city: Seoul

first: miwha

last: Chang

address: anam dong 5ga

department: School of Life Sciences and Biotechnology

institute: Korea university

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring 7.3.1 (Agilent Technologies, USA).

organism: Saccharomyces cerevisiae

source_name: total RNA Saccharomyces cerevisiae wild type

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for CosR-knockdown) or Cy3-dUTP (for the wild type).

growth_protocol: Yeast cell was grown on SD-ura medium. Yeast cell was grown overnight at 30°C . The culture was refreshed to 0.2 O.D and grown at 30°C  for 5h 30min. Cells were collected.

extract_protocol: Total RNA was isolated using TRIzol reagent (Life Technologies). RNA concentrations were determined by measuring absorbance at 260nm.

treatment_protocol: KDX1 was subcloned into yeast multicopy vector ( pRS426 )

tag: genotype/variation

source_name: total RNA Saccharomyces cerevisiae KDX1 over-expressed strain

value: KDX1 over-expressed strain


title: 18q-223c

source_name: patient genomic DNA

source_name: Normal control DNA


title: 18q-207c


title: A549, H1N1, 24hpi (rep3)

description:
Human influenza-infected cells
Sample name: H1C

value: H1N1 (A/PuertoRico/8/34)


title: 18q-6c


title: high R/FR_SA spray, biological rep 1

value: petiole