title: 3h Submerged Arabidopsis (c-myc tagged WRKY22/Columbia) Replicate 6

tag: genotype


title: NOD.Tconv.Rep3.Tech1

status: Public on Jul 03 2013

type: RNA

city: London

first: MARC

last: MARTINEZ-LLORDELLA

address: 3rd Floor Cheyne Wing, Denmark Hill

department: Liver Science Department

country: United Kingdom

institute: King's College London

description:
Gene expression from sorted T cells
NOD_Toe6_Tconv

hyb_protocol: aRNA was hybridized to 4x44K Mouse Whole Genome Microarrays (Agilent) for 18 hours following the manufacturer’s protocol.

scan_protocol: Microarrays were washed in 0.01x SSC/0.005% Triton X-102 at 40ºC, dried with HEPA filtered compressed nitrogen and scanned on an Agilent Technologies DNA Microarray Scanner at 5um resolution.

data_processing: The scanned images were analyzed with GeneSpring GX Software (Agilent) using default parameters.

molecule: total RNA

organism: Mus musculus

source_name: conventional T cells from NOD mouse. Biological replicate 3. Technical replicate 1.

label_protocol: Total RNA was  labeled using a modified protocol with the ULS aRNA Fluorescent Cy5 labeling kit (Kreatech Diagnostics, The Netherlands) and purified using RNA Clean and Concentrate spin columns according to manufacturer’s protocol (Zymo Research Corporation, Orange CA)

growth_protocol: All Foxp3+ Tregs were freshely sorted using Foxp3.GFP or based on CD25+GITRhi staining. CD4+CD25-GITR- cells were used as Tconv cells. RNA was isolated from ~30,000 cells and used for microarray analysis.

extract_protocol: Spleen and LN cells were used for sorting Tregs.

tag: strain

value: NOD

tag: t cell type

value: Sorted CD4+ conventional T cells from spleen and lymph nodes


title: 3h Submerged Arabidopsis (c-myc tagged WRKY22/Columbia) Replicate 2

type: genomic

city: Taipei

first: Fu-Chiun

last: Hsu

address: No. 128, Sec. 2, Academia Road, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

description: ChIP-chip c-myc tagged WRKY22/ Columbia (Cy5/Cy3) with anti-c-myc antibody (9E10)

hyb_protocol: The labeled DNA was hybridized to NimbleGen A. thaliana ChIP-chip 385K Minimal Promoter Arrays (NimbleGen).  The hybridization and washing of arrays were performed following the Nimblegen standard operating protocols (www.nimblegen.com).

scan_protocol: Array images were acquired with Axon GenePix 4000B and GenePix 6.0 software (Axon Instruments, Inc., Union City, CA, USA).

data_processing: The images were then converted to scaled Log2-ratio of the probes for peak finding analysis according to the genomic position in NimbleScan software (NimbleGen).  Peaks of enriched DNA fragments were identified and mapped to promoters in the Arabidopsis genome using the default setting in the NimbleScan software (NimbleGen) according to the manufacturer’s description.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 3h Submerged Arabidopsis (c-myc tagged WRKY22)

label_protocol: One hundred pg of DNA was amplified using the GenomePlex Whole Genome Amplification Kit (Sigma-Aldrich, St. Louis, MO, USA) according to the manufacturer’s instructions.  The amplified DNA was then purified using the QIAquick PCR cleanup kit (Qiagen).  The purified DNA was quantified using a Nanodrop spectrophotometer and labeled with Cy3 (for Columbia) and Cy5 (for WRKY22-18×c-myc in wrky22-ko2) fluorescent dyes.   Labeling experiments were performed at the DNA Microarray Core facility, Institute of Plant and Microbial Biology, Academia Sinica, as described on http://ipmb.sinica.edu.tw/microarray/protocol.htm.

growth_protocol: Transgenic lines expressing c-myc tagged WRKY22 in wrky22-ko2 background plants were generated using a T-DNA insertion containing 1000 bp of upstream promoter sequence and WRKY22 full-length genomic DNA in frame with 18 copies of c-myc sequence at 3’ end in a pMDC110 derived binary vector.  The recombinant plasmid was then mobilized into Agrobacterium tumefaciens strain GV3101 and the resulting GV3101 strain was used to transform wrky22-ko2 plants through floral dipping.  Seeds were sown on plates with 0.55% of phytagel (Sigma-Aldrich, St. Louis, MO, USA) in half-strength MS medium (Duchefa Biochemie BV, Haarlem, Netherlands) containing 0.5% sucrose at pH 5.7, and kept at 4oC in the dark for 3 days to achieve uniform germination.  The plates were then transferred to a growth chamber and placed vertically, and plants were grown at 22ºC under a 16-hour light (81 μmol s-1 m-2)/8-hour dark cycle.  5-day-old seedlings were transplanted onto fresh plates and the plates were placed vertically to prevent roots from growing into medium.  The transplanted seedlings were grown in the growth chamber until they were 14-day-old.

extract_protocol: Protocols describing materials and methods for ChIP have previously been described in detail by Kaufmann et al. (2010).  Briefly, 1.5 g of 14-day-old seedlings was chemically crosslinked by the addition of 1% formaldehyde for 15 minutes at room temperature.  The fixed seedlings were rinsed five times with MC buffer (10 mM sodium phosphate, pH 7, 50 mM NaCl and 0.1 M sucrose) and frozen in liquid nitrogen.  The frozen samples were homogenized, filtered, centrifuged and washed to isolate nuclei.  The nuclear pellets were resuspended, lysed and sonicated to shear crosslinked DNA.  The sonication was carried out with a Bioruptor UCD-200 (Diagenode, Liège, Belgium) until the average size of sheared DNA was approximately 500 bp.  The sonicated chromatin was pre-cleared with protein-A agarose beads for 1 hour and immunoprecipitated with 2 μg of anti-c-myc antibody for 2 hours followed by addition of protein-A agarose beads for 3 hours.  The beads were washed five times with IP buffer (50 mM HEPES, pH 7.5, 150 mM NaCl, 5 mM MgCl2, 10 μM ZnSO4, 1% Triton X-100 and 0.05% SDS).  The bound IP complexes were eluted with elution buffer (0.1 M glycine, 0.5 M NaCl and 0.05% Tween-20, pH 2.8) and neutralized with 1 M Tris, pH 9.0.  The eluantes were digested with proteinase K overnight at 37 oC to remove proteins followed by incubation at 65 oC for at least 6 hours to reverse crosslinking.  The reverse crosslinked DNA was then purified by extraction with phenol:chloroform:isoamyl alcohol and ethanol precipitation in the presence of glycogen.  The DNA pellets were washed with 70 % of ethanol, air dried and resuspended in TE 8.0.

treatment_protocol: Plates with plants on the surface of the medium were placed into half-strength MS liquid medium that was bubbled with 3 % oxygen balanced with nitrogen for 3h.  The liquid MS medium was pretreated with 3% oxygen for one hour before use.

tag: treatment

value: submerged for 3h

value: c-myc tagged WRKY22

tag: genetic background

value: Columbia

tag: age

tag: tissue

value: seedling

tag: chip antibody

tag: chip antibody manufacturer

value: The Developmental Studies Hybridoma Bank (DSHB), University of Iowa, USA

source_name: 3h Submerged Arabidopsis (Columbia)

value: wt


title: LUNG 245A_d3PR8 (4225362017_C)

city: Bethesda

first: Marlene

last: Brandes

state: MD

address: 9000 Rockville Pike

department: Laboratory of Systems Biology

country: USA

institute: NIH, NIAID

description:
4225362017_C
Amp batch 1 - BioRep1 - Hyb batch 5

hyb_protocol: 1.2ug of the biotinylated sample was used for hybridization. Hybridization conditions were adjusted according to NuGen's Illumina Solution application notes 2, or else the standard Illumina hybridization protocol was followed.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were log2-transformed and normalised by quantile normalisation with GenePattern.

label: Biotin

source_name: mouse 245 lung, H1N1 influenza A infected, batch A

label_protocol:
Biotinylated cDNA were prepared after amplification with the Ovation RNA Amplification System V2 (NuGEN Technologies).
5ug of the amplified product was used for UNG-based abasic site abrasion and biotinylation according NuGen's Illumina Solution application notes 2.

extract_protocol: Preserved whole lung pieces were homogenized in Trizol and total RNA was extracted, followed by clean-up and DNase I treatment with the QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol:
5- to 8-week-old male C57BL/6 were intranasally infected with 0.6LD50 of the mouse pathogenic H1N1 influenza A virus PR8 under light isoflurane anesthesia. Infectious doses were supplied in a volume of 50ul sterile pharmaceutical-grade physiological saline.
Lungs were harvested at various time points post infection. Immediately after euthanasia, lungs were perfused in situ via the right cardiac ventricle with PBS/EDTA (10mM) pre-warmed to 37°C and then immediately processed for down-stream applications.
Entire lungs were immediately transferred into 1.5ml RNAlater (Ambion), chopped into small pieces, left at 4°C overnight and then placed at -20°C for prolonged storage.

value: 5-8 weeks

tag: Sex

value: male

value: whole lung

tag: perturbation

value: H1N1 influenza A 0.6LD50 PR8

tag: time post-infection

value: 3 days

tag: mouse id


title: NOD.Tconv.Rep2.Tech2

description:
Gene expression from sorted T cells
NOD_Toe1b_Tconv

source_name: conventional T cells from NOD mouse. Biological replicate 2. Technical replicate 2.


title: 1B3.RAGKO.Treg.Rep4.Tech2

description:
Gene expression from sorted T cells
1B3.RAG_KO_Toe12_Tregs

source_name: regulatory T cells from 1B3.RAGKO transgenic mouse. Biological replicate 4. Technical replicate 2.

value: 1B3.RAGKO transgenic

value: Sorted CD4+ regulatory T cells from spleen and lymph nodes


title: NOD.Tconv.Rep1.Tech2

description:
Gene expression from sorted T cells
NOD_Toe1a_Tconv

source_name: conventional T cells from NOD mouse. Biological replicate 1. Technical replicate 2.


title: NOD.Tconv.Rep1.Tech1

source_name: conventional T cells from NOD mouse. Biological replicate 1. Technical replicate 1.


title: NOD.Tconv.Rep2.Tech1

source_name: conventional T cells from NOD mouse. Biological replicate 2. Technical replicate 1.


title: 3h Submerged Arabidopsis (c-myc tagged WRKY22/Columbia) Replicate 1

growth_protocol: Transgenic lines expressing c-myc tagged WRKY22 in wrky22-ko2 background plants were generated using a T-DNA insertion containing 1000 bp of upstream promoter sequence and WRKY22 full-length genomic DNA in frame with 18 copies of c-myc sequence at 3' end in a pMDC110 derived binary vector.  The recombinant plasmid was then mobilized into Agrobacterium tumefaciens strain GV3101 and the resulting GV3101 strain was used to transform wrky22-ko2 plants through floral dipping.  Seeds were sown on plates with 0.55% of phytagel (Sigma-Aldrich, St. Louis, MO, USA) in half-strength MS medium (Duchefa Biochemie BV, Haarlem, Netherlands) containing 0.5% sucrose at pH 5.7, and kept at 4oC in the dark for 3 days to achieve uniform germination.  The plates were then transferred to a growth chamber and placed vertically, and plants were grown at 22ºC under a 16-hour light (81 μmol s-1 m-2)/8-hour dark cycle.  5-day-old seedlings were transplanted onto fresh plates and the plates were placed vertically to prevent roots from growing into medium.  The transplanted seedlings were grown in the growth chamber until they were 14-day-old.


title: 1B3.RAGKO.Treg.Rep4.Tech1

source_name: regulatory T cells from 1B3.RAGKO transgenic mouse. Biological replicate 4. Technical replicate 1.


title: Lung 246A_d3PR8 (4225362016_A)

description:
4225362016_A
Amp batch 1 - BioRep2 - Hyb batch 4

source_name: mouse 246 lung, H1N1 influenza A infected, batch A


title: 1B3.RAGKO.Treg.Rep3.Tech1

description:
Gene expression from sorted T cells
1B3.RAG_KO_Toe10_Tregs

source_name: regulatory T cells from 1B3.RAGKO transgenic mouse. Biological replicate 3. Technical replicate 1.


title: Lung 246A_d3PR8 (4225362014_E)

description:
4225362014_E
Amp batch 1 - BioRep2 - Hyb batch 4


title: 1B3.RAGKO.Treg.Rep3.Tech2

source_name: regulatory T cells from 1B3.RAGKO transgenic mouse. Biological replicate 3. Technical replicate 2.


title: Lung 246C_d3PR8 (4225362014_F)

description:
4225362014_F
Amp batch 3 - BioRep2 - Hyb batch 4

source_name: mouse 246 lung, H1N1 influenza A infected, batch C


title: Lung 247C_d3PR8 (4225362014_D)

description:
4225362014_D
Amp batch 3 - BioRep3 - Hyb batch 4

source_name: mouse 247 lung, H1N1 influenza A infected, batch C


title: Lung 247A_d3PR8 (4225362016_B)

description:
4225362016_B
Amp batch 1 - BioRep3 - Hyb batch 4

source_name: mouse 247 lung, H1N1 influenza A infected, batch A


title: 3h Submerged Arabidopsis (c-myc tagged WRKY22/Columbia) Replicate 4

growth_protocol: Seeds were sown on plates with 0.55% of phytagel (Sigma-Aldrich, St. Louis, MO, USA) in half-strength MS medium (Duchefa Biochemie BV, Haarlem, Netherlands) containing 0.5% sucrose at pH 5.7, and kept at 4oC in the dark for 3 days to achieve uniform germination.  The plates were then transferred to a growth chamber and placed vertically, and plants were grown at 22ºC under a 16-hour light (81 μmol s-1 m-2)/8-hour dark cycle.  5-day-old seedlings were transplanted onto fresh plates and the plates were placed vertically to prevent roots from growing into medium.  The transplanted seedlings were grown in the growth chamber until they were 14-day-old.


title: Lung 247A_d3PR8 (4225362014_A)

description:
4225362014_A
Amp batch 1 - BioRep3 - Hyb batch 4


title: Lung 245B_d3PR8 (4225362014_B)

description:
4225362014_B
Amp batch 2 - BioRep1 - Hyb batch 4

source_name: mouse 245 lung, H1N1 influenza A infected, batch B


title: 1B3.RAGKO.Treg.Rep2.Tech2

description:
Gene expression from sorted T cells
1B3.RAG_KO_0b_Tregs

source_name: regulatory T cells from 1B3.RAGKO transgenic mouse. Biological replicate 2. Technical replicate 2.


title: Lung 245C_d3PR8 (4225362014_C)

description:
4225362014_C
Amp batch 3 - BioRep1 - Hyb batch 4

source_name: mouse 245 lung, H1N1 influenza A infected, batch C


title: 1B3.RAGKO.Tconv.Rep3.Tech2

description:
Gene expression from sorted T cells
1B3.RAG_KO_Toe12_Tconv

source_name: conventional T cells from 1B3.RAGKO transgenic mouse. Biological replicate 3. Technical replicate 2.


title: 1B3.RAGKO.Tconv.Rep2.Tech2

description:
Gene expression from sorted T cells
1B3.RAG_KO_Toe10_Tconv

source_name: conventional T cells from 1B3.RAGKO transgenic mouse. Biological replicate 2. Technical replicate 2.


title: 260 Lungd3PR8_II2 (4225362013_D)

description:
4225362013_D
RNA batch 2 - Amp batch 2 - Hyb batch 2

source_name: mouse 260 lung, H1N1 influenza A infected, batch II2


title: 1B3.RAGKO.Treg.Rep2.Tech1

source_name: regulatory T cells from 1B3.RAGKO transgenic mouse. Biological replicate 2. Technical replicate 1.


title: 1B3.RAGKO.Treg.Rep1.Tech1

description:
Gene expression from sorted T cells
1B3.RAG_KO_0a_Tregs

source_name: regulatory T cells from 1B3.RAGKO transgenic mouse. Biological replicate 1. Technical replicate 1.


title: 1B3.RAGKO.Treg.Rep1.Tech2

source_name: regulatory T cells from 1B3.RAGKO transgenic mouse. Biological replicate 1. Technical replicate 2.


title: 260 Lungd3PR8_I2 (4225362013_E)

description:
4225362013_E
RNA batch 1 - Amp batch 2 - Hyb batch 2

source_name: mouse 260 lung, H1N1 influenza A infected, batch I2


title: 260 Lungd3PR8_III1 (4225362013_A)

description:
4225362013_A
RNA batch 3 - Amp batch 1 - Hyb batch 2

source_name: mouse 260 lung, H1N1 influenza A infected, batch III1


title: 260 Lungd3PR8_II1 (4225362013_C)

description:
4225362013_C
RNA batch 2 - Amp batch 1 - Hyb batch 2

source_name: mouse 260 lung, H1N1 influenza A infected, batch II1


title: 1B3.RAGKO.Tconv.Rep1.Tech2

description:
Gene expression from sorted T cells
1B3.RAG_KO_0b_Tconv

source_name: conventional T cells from 1B3.RAGKO transgenic mouse. Biological replicate 1. Technical replicate 2.


title: 260 Lungd3PR8_III1 (4225362033_B)

description:
4225362033_B
RNA batch 3 - Amp batch 1 - Hyb batch 1


title: 260 Lungd3PR8_I2 (4225362031_F)

description:
4225362031_F
RNA batch 1 - Amp batch 2 - Hyb batch 1


title: 1B3.Treg.Rep3.Tech2

description:
Gene expression from sorted T cells
1B3_Toe5_Tregs

source_name: regulatory T cells from 1B3 transgenic mouse. Biological replicate 3. Technical replicate 2.

value: 1B3 transgenic


title: 260 Lungd3PR8_I1 (4225362013_B)

description:
4225362013_B
RNA batch 1 - Amp batch 1 - Hyb batch 2

source_name: mouse 260 lung, H1N1 influenza A infected, batch I1


title: 1B3.RAGKO.Tconv.Rep2.Tech1

source_name: conventional T cells from 1B3.RAGKO transgenic mouse. Biological replicate 2. Technical replicate 1.


title: 1B3.Treg.Rep2.Tech1

description:
Gene expression from sorted T cells
1B3_Toe14_Tregs

source_name: regulatory T cells from 1B3 transgenic mouse. Biological replicate 2. Technical replicate 1.


title: 260 Lungd3PR8_II2 (4225362033_F)

description:
4225362033_F
RNA batch 2 - Amp batch 2 - Hyb batch 1


title: 1B3.RAGKO.Tconv.Rep1.Tech1

source_name: conventional T cells from 1B3.RAGKO transgenic mouse. Biological replicate 1. Technical replicate 1.


title: 1B3.RAGKO.Tconv.Rep3.Tech1

source_name: conventional T cells from 1B3.RAGKO transgenic mouse. Biological replicate 3. Technical replicate 1.


title: 1B3.Treg.Rep3.Tech1

source_name: regulatory T cells from 1B3 transgenic mouse. Biological replicate 3. Technical replicate 1.


title: 260 Lungd3PR8_III2 (4225362013_F)

description:
4225362013_F
RNA batch 3 - Amp batch 2 - Hyb batch 2

source_name: mouse 260 lung, H1N1 influenza A infected, batch III2


title: 260 Lungd3PR8_I2 (4225362033_D)

description:
4225362033_D
RNA batch 1 - Amp batch 2 - Hyb batch 1


title: 260 Lungd3PR8_II2 (4225362031_E)

description:
4225362031_E
RNA batch 2 - Amp batch 2 - Hyb batch 1


title: 1B3.Treg.Rep1.Tech2

description:
Gene expression from sorted T cells
1B3_Toe10_Tregs

source_name: regulatory T cells from 1B3 transgenic mouse. Biological replicate 1. Technical replicate 2.


title: 260 Lungd3PR8_II1 (4225362033_A)

description:
4225362033_A
RNA batch 2 - Amp batch 1 - Hyb batch 1


title: 260 Lungd3PR8_III2 (4225362031_D)

description:
4225362031_D
RNA batch 3 - Amp batch 2 - Hyb batch 1


title: 1B3.Treg.Rep1.Tech1

source_name: regulatory T cells from 1B3 transgenic mouse. Biological replicate 1. Technical replicate 1.


title: 1B3.Tconv.Rep3.Tech2

description:
Gene expression from sorted T cells
1B3_Toe14_Tconv

source_name: conventional T cells from 1B3 transgenic mouse. Biological replicate 3. Technical replicate 2.


title: 1B3.Tconv.Rep4.Tech2

description:
Gene expression from sorted T cells
1B3_Toe5_Tconv

source_name: conventional T cells from 1B3 transgenic mouse. Biological replicate 4. Technical replicate 2.


title: 260 Lungd3PR8_I1 (4225362031_A)

description:
4225362031_A
RNA batch 1 - Amp batch 1 - Hyb batch 1


title: 1B3.Tconv.Rep2.Tech2

description:
Gene expression from sorted T cells
1B3_Toe10_Tconv

source_name: conventional T cells from 1B3 transgenic mouse. Biological replicate 2. Technical replicate 2.


title: 260 Lungd3PR8_II1 (4225362031_B)

description:
4225362031_B
RNA batch 2 - Amp batch 1 - Hyb batch 1


title: 1B3.Tconv.Rep2.Tech1

source_name: conventional T cells from 1B3 transgenic mouse. Biological replicate 2. Technical replicate 1.


title: 1B3.Tconv.Rep3.Tech1

source_name: conventional T cells from 1B3 transgenic mouse. Biological replicate 3. Technical replicate 1.


title: 260 Lungd3PR8_I1 (4225362033_C)

description:
4225362033_C
RNA batch 1 - Amp batch 1 - Hyb batch 1


title: 260 Lungd3PR8_III1 (4225362031_C)

description:
4225362031_C
RNA batch 3 - Amp batch 1 - Hyb batch 1

source_name: mouse 260 lung, H1N1 influenza A infected, batch III1


title: MB231 [H3K4me3]

city: Tucson

first: Lukas

last: Vrba

state: AZ

address: 1515 N Campbell Ave

department: Arizona Cancer Center

institute: University of Arizona

description: breast carcinoma cell line

hyb_protocol: Combined Cy3 and Cy5 labeled samples were vaccum concentrated to volume of 91.5 µl.  12.5 µl of human Cot-1 DNA (1µg/µl, Invitrogen Cat. No. 15279-011), 26 µl of Agilent blocking agent (10x) and 130 µl of Agilent hybridization buffer (2x) were added.  Samples were heated for 3 min at 95 oC, transferred to 37 oC, incubated for 30 min, and then used for microarray hybridization for 28h at 65 oC.  After hybridization, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 for 5 min at room temperature, then in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 2 for 5 min at 37 oC, washed in acetronitrile for 10 s at room temperature and finally in stabilization and drying solution for 30 s at room temperature.

scan_protocol: Slides were scanned using an Axon GenePix 4000B microarray scanner (Axon Instruments, Inc., Foster City, CA, USA) and GenePix 6.0 software at 5 µm resolution and PMT settings 750 (635nm) and 600 (532nm)

data_processing: Output from GenePix (*.gpr files) were imported to R using the limma package.  Individual channels were first spatially normalized within arrays using ma2D function from the package marray and then loess normalized between arrays using the function normalize.loess from package affy.  The RG object was transformed to an MA object and M values were again loess normalized between arrays.

organism: Homo sapiens

source_name: [IP DNA] H3K4me3_MB231

label_protocol: DNA amplification was based on random prime synthesis using the BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA). The DNA sample or equivalent amount of input in a total volume of 21 ul was mixed with 20 ul of 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min. 5 ul of 10x dUTP Nucleotide Mix, 3 ul of 1 mM dTTP and 1 ul of Exo-Klenow Fragment, were added and incubated at 37 C for 20 h. Amplified DNA was purified using a QIAquick PCR purification kit (Qiagen, Valencia, CA) and quantified on a ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). The typical yield was 4-5 ug of amplified DNA per 50 ul reaction.  Equal amounts (2 ug) of amplified immunoprecipitated and input DNA were labeled using the BioPrime DNA Labeling System (Invitrogen) with Cy3 or Cy5 dyes respectively. DNA in a volume of 42 ul was mixed with 40 ul 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min.  10 ul of 10x dUTP Nucleotide Mix, 4 ul of 1 mM dTTP, 2 ul of Cy3- or Cy5-dUTP (1mM) (GE healthcare, Piscataway, NJ, USA) and 2 ul of Exo-Klenow Fragment were added and the mixture was incubated for 20 h at 37 C.  Labeled targets were purified using the QIAquick PCR purification kit (Qiagen).  The efficiency of labeling was determined using ND-1000 spectrophotometer (Nanodrop Technologies).  The typical yield was 200 - 300 pmol of dye incorporated in 7 - 8 ug of DNA per sample.

growth_protocol: RPMI 1640 medium supplemented with 5% FBS, 100 units/ml penicillin and 50 μg/ml streptomycin

extract_protocol:
Wash ~2x107 cells in a tissue culture dishes with 10 ml of HBSS (Hanks Balanced Salt Solution) with 2.5mM EDTA. Add 15 ml of HBSS with 2.5mM EDTA, with 400 ul of 37% formaldehyde added (final conc 1%).  Incubate at 37 C for 10 minutes. Aspirate off formaldehyde solution and add 5 ml of ice cold HBSS, 2.5mM EDTA with protease inhibitors (PIs) at a final concentration of 1 mM PMSF, 1 ug/ml Pepstatin A, 1 ug/ml Aprotinin. Gently detach cells with a cell scraper and transfer the cells to a conical tube.  Wash remaining cells out of flask with 5 ml of HBSS with PIs. Spin cells down ~700 g for 5 min at 4 C. After spin, aspirate HBSS then add PIPES buffer (5 mM PIPES buffer pH 8.0, 85mM KCl, 0.5% NP40) with protease inhibitors 400 ul/sample, transfer sample to microfuge tube, then incubate on ice for 10 min. After incubation, pellet cells at 700 g for 5 min at 4 C. Remove PIPES buffer and add SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) with protease inhibitors. Again 10 min on ice. Store at -80 C. Thaw samples on ice. Sonicate samples 6 x for 10 seconds on setting 7-8 watts until the majority of chromatin is between 500-1000 bp in length when checked on 1% agarose gel. After sonication spin samples at max speed at 4 C for 10 min to remove any cellular debris.  Dilute supernatant fraction 10 fold with ChIPs dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl) with PIs.  Set aside 10 % of sample into a fresh microfuge tube - Input sample.
[immunoprecipitation protocol] Pre-clear the diluted sample by adding 120 ul of protein-A sepharose slurry (Pharmacia).  Rotate for 1hr at 4 C. Spin down samples at 400 g at 4 C for 2 min to pellet beads. Divide samples equally into microfuge tubes for each Ab sample and add Abs. Rotate tubes overnight at 4 C. Next day add 90 ul of Pro-A sepharose slurry to each Ab tube. Rotate at 4 C for 1hr.  Spin samples in picofuge for 10 s, discard all but 400 ul of supernatant, resuspend sepahrose beads in remaining volume and transfer to Handee spin cup columns (Pierce), spin in picofuge for 10 s, discard flow through. Wash beads for 5 min at 4 C with 400 ul each of the following buffers:  low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA with 250 ul of elution buffer (1% SDS, 0.1M NaHCO3).  Mix well and rotate for 15 min at room temp.  Spin down, save flow through to a new microfuge tube. Repeat elution and combine eluates.  Total volume ~ 500 ul. Bring the Input sample volume up to 500 ul using the elution buffer. To reverse the cross-links add 40 ul of 5M NaCl to eluate or diluted input and incubate at 65 C for 4 hr. After incubation add 100 ul of 0.1M EDTA, 40 ul of 1M Tris-Cl pH 7.5, and 2 ul of 20 mg/ml proteinase K to each sample and incubate at 45 C for 1 hr. Purify samples using QIAquick PCR purification kit (Qiagen, Valencia, CA): Transfer samples to 10 ml tubes. Add 5 volumes of PB buffer, mix well, apply to Qiagen columns under vacuum, wash 2x with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

tag: specimen

value: mammary gland

tag: cell type

value: breast carcinoma cell line

value: anti-H3K4me3 (Millipore, Vat# 05-745R, Lot# DAM1576962)

source_name: [Input DNA] H3K4me3_MB231


title: 184D-p16sh [H3K4me3]

description: Post-Stasis human mammary epithelial cells

source_name: [IP DNA] H3K4me3_184D-p16sh

growth_protocol: M87A medium supplemented with oxytocin and cholera toxin at 0.5 ng/ml

source_name: [Input DNA] H3K4me3_184D-p16sh


title: 1B3.Tconv.Rep1.Tech1

description:
Gene expression from sorted T cells
1B3_6135_Tconv

source_name: conventional T cells from 1B3 transgenic mouse. Biological replicate 1. Technical replicate 1.

value: Sorted CD4+ conventional T cells from spleen and lymph nodes


title: BT549 [H3K4me3]

description: breast carcinoma cell line

source_name: [IP DNA] H3K4me3_BT549

source_name: [Input DNA] H3K4me3_BT549


title: 1B3.Tconv.Rep1.Tech2

source_name: conventional T cells from 1B3 transgenic mouse. Biological replicate 1. Technical replicate 2.


title: 184D_EP [H3K4me3]

description: Pre-Stasis human mammary epithelial cells

source_name: [IP DNA] H3K4me3_184D_EP

source_name: [Input DNA] H3K4me3_184D_EP


title: 184Aa [H3K4me3]

source_name: [IP DNA] H3K4me3_184Aa

value: Post-Stasis human mammary epithelial cells

source_name: [Input DNA] H3K4me3_184Aa


title: MB231 [H3K27me3]

description: breast carcinoma cell line

source_name: [IP DNA] H3K27me3_MB231

extract_protocol:
Wash ~2x107 cells in a tissue culture dishes with 10 ml of HBSS (Hanks Balanced Salt Solution) with 2.5mM EDTA. Add 15 ml of HBSS with 2.5mM EDTA, with 400 ul of 37% formaldehyde added (final conc 1%).  Incubate at 37 C for 10 minutes. Aspirate off formaldehyde solution and add 5 ml of ice cold HBSS, 2.5mM EDTA with protease inhibitors (PIs) at a final concentration of 1 mM PMSF, 1 ug/ml Pepstatin A, 1 ug/ml Aprotinin. Gently detach cells with a cell scraper and transfer the cells to a conical tube.  Wash remaining cells out of flask with 5 ml of HBSS with PIs. Spin cells down ~700 g for 5 min at 4 C. After spin, aspirate HBSS then add PIPES buffer (5 mM PIPES buffer pH 8.0, 85mM KCl, 0.5% NP40) with protease inhibitors 400 ul/sample, transfer sample to microfuge tube, then incubate on ice for 10 min. After incubation, pellet cells at 700 g for 5 min at 4 C. Remove PIPES buffer and add SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) with protease inhibitors. Again 10 min on ice. Store at -80 C. Thaw samples on ice. Sonicate samples 6 x for 10 seconds on setting 7-8 watts until the majority of chromatin is between 500-1000 bp in length when checked on 1% agarose gel. After sonication spin samples at max speed at 4 C for 10 min to remove any cellular debris.  Dilute supernatant fraction 10 fold with ChIPs dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl) with PIs.  Set aside 10 % of sample into a fresh microfuge tube - Input sample.
[immunoprecipitation protocol ] Pre-clear the diluted sample by adding 120 ul of protein-A sepharose slurry (Pharmacia).  Rotate for 1hr at 4 C. Spin down samples at 400 g at 4 C for 2 min to pellet beads. Divide samples equally into microfuge tubes for each Ab sample and add Abs. Rotate tubes overnight at 4 C. Next day add 90 ul of Pro-A sepharose slurry to each Ab tube. Rotate at 4 C for 1hr.  Spin samples in picofuge for 10 s, discard all but 400 ul of supernatant, resuspend sepahrose beads in remaining volume and transfer to Handee spin cup columns (Pierce), spin in picofuge for 10 s, discard flow through. Wash beads for 5 min at 4 C with 400 ul each of the following buffers:  low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA with 250 ul of elution buffer (1% SDS, 0.1M NaHCO3).  Mix well and rotate for 15 min at room temp.  Spin down, save flow through to a new microfuge tube. Repeat elution and combine eluates.  Total volume ~ 500 ul. Bring the Input sample volume up to 500 ul using the elution buffer. To reverse the cross-links add 40 ul of 5M NaCl to eluate or diluted input and incubate at 65 C for 4 hr. After incubation add 100 ul of 0.1M EDTA, 40 ul of 1M Tris-Cl pH 7.5, and 2 ul of 20 mg/ml proteinase K to each sample and incubate at 45 C for 1 hr. Purify samples using QIAquick PCR purification kit (Qiagen, Valencia, CA): Transfer samples to 10 ml tubes. Add 5 volumes of PB buffer, mix well, apply to Qiagen columns under vacuum, wash 2x with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

value: anti-H3K27me3 (Millipore, Cat# 07-449, Lot# DAM1588246)

source_name: [Input DNA] H3K27me3_MB231


title: 184_FB [H3K4me3]

description: Human mammary fibroblast cells

source_name: [IP DNA] H3K4me3_184_FB

growth_protocol: DMEM/F12 with 10% FBS

value: Human mammary fibroblast cells

source_name: [Input DNA] H3K4me3_184_FB


title: 184B [H3K4me3]

description: Post-Selection human mammary epithelial cells

source_name: [IP DNA] H3K4me3_184B

source_name: [Input DNA] H3K4me3_184B


title: 48RT_EP [H3K4me3]

source_name: [IP DNA] H3K4me3_48RT_EP

value: Pre-Stasis human mammary epithelial cells

source_name: [Input DNA] H3K4me3_48RT_EP


title: 240LB_EP [H3K4me3]

source_name: [IP DNA] H3K4me3_240LB_EP

source_name: [Input DNA] H3K4me3_240LB_EP


title: MCF7 [H3K4me3]

description: breast carcinoma cell line

source_name: [IP DNA] H3K4me3_MCF7

source_name: [Input DNA] H3K4me3_MCF7


title: MB453 [H3K4me3]

description: breast carcinoma cell line

source_name: [IP DNA] H3K4me3_MB453

source_name: [Input DNA] H3K4me3_MB453


title: 184A1 [H3K4me3]

description: Immortal human mammary epithelial cells

source_name: [IP DNA] H3K4me3_184A1

value: Immortal human mammary epithelial cells

source_name: [Input DNA] H3K4me3_184A1


title: MB453 [H3K27me3]

description: breast carcinoma cell line

source_name: [IP DNA] H3K27me3_MB453

source_name: [Input DNA] H3K27me3_MB453


title: 240L_FB [H3K4me3]

description: Human mammary fibroblast cells

source_name: [IP DNA] H3K4me3_240L_FB

source_name: [Input DNA] H3K4me3_240L_FB


title: 184A1 [H3K27me3]

description: Immortal human mammary epithelial cells

source_name: [Input DNA] H3K27me3_184A1


title: BT549 [H3K27me3]

description: breast carcinoma cell line

source_name: [IP DNA] H3K27me3_BT549

source_name: [Input DNA] H3K27me3_BT549


title: MCF7 [H3K27me3]

description: breast carcinoma cell line

source_name: [IP DNA] H3K27me3_MCF7

source_name: [Input DNA] H3K27me3_MCF7


title: 48L_FB [H3K4me3]

description: Human mammary fibroblast cells

source_name: [IP DNA] H3K4me3_48L_FB

source_name: [Input DNA] H3K4me3_48L_FB


title: 184D-p16sh [H3K27me3]

source_name: [IP DNA] H3K27me3_184D-p16sh

source_name: [Input DNA] H3K27me3_184D-p16sh


title: relA spoT LSP 3

type: mixed

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

institute: Institute of Food Research

hyb_protocol: Slides blocked with DCE according to protocol at PMID 11266573. For hybridisation and washing protocols see http://www.ifr.ac.uk/safety/Microarrays/protocols.html

scan_protocol: Axon GenePix4000A 10 µm resolution scan and see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated usiong GenePix (Molecular Devices) .

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 3.6 replicate 3

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: Salmonella strains were innoculated 1/100 from 5 ml over night cultures into 25 ml Lb (10g NaCl) in 250 ml flasksand grown at 37°C in a shaking water bath. When the required OD600 was reached 10 ml culture was removed and mixed with 2 ml 5% Phenol, 95% Ethanol, shaken for 20 seconds then stored on ice for 20 min. Cells were then harvested by centrifugation and RNA extracted.

extract_protocol: Extraction protocols at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

tag: growth phase

value: late stationary

tag: genotype/variation

value: ∆relA, ∆spoT

source_name: SL1344 genomic DNA


title: 184Aa [H3K27me3]

source_name: [IP DNA] H3K27me3_184Aa

source_name: [Input DNA] H3K27me3_184Aa


title: 260 Lungd3PR8_III2 (4225362033_E)

description:
4225362033_E
RNA batch 3 - Amp batch 2 - Hyb batch 1

source_name: mouse 260 lung, H1N1 influenza A infected, batch III2

value: 5-8 weeks

value: male

value: whole lung


title: 240LB_EP [H3K27me3]

source_name: [IP DNA] H3K27me3_240LB_EP

source_name: [Input DNA] H3K27me3_240LB_EP


title: 184_FB [H3K27me3]

description: Human mammary fibroblast cells

source_name: [IP DNA] H3K27me3_184_FB

source_name: [Input DNA] H3K27me3_184_FB


title: 240L_FB [H3K27me3]

description: Human mammary fibroblast cells

source_name: [IP DNA] H3K27me3_240L_FB

source_name: [Input DNA] H3K27me3_240L_FB


title: 184D_EP [H3K27me3]

source_name: [IP DNA] H3K27me3_184D_EP

source_name: [Input DNA] H3K27me3_184D_EP


title: 184B [H3K27me3]

source_name: [IP DNA] H3K27me3_184B

value: Post-Selection human mammary epithelial cells

source_name: [Input DNA] H3K27me3_184B


title: MB453 [DNAmet]

description: breast carcinoma cell line

source_name: [IP DNA] DNAmet_MB453

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen). 5 μg of RNase treated DNA was dried under vacuum and resuspended with 50 μl SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and 450 μl of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl).  Vortex for ~20 minutes to fully resuspend the DNA. Sonicate the samples 5x for 10 seconds (5 times total) at 8 watts.  Make sure that most of the DNA is between 300-600 bp long.  Set aside 50 μl of sample in a new microfuge tube - Input DNA.
[immunoprecipitation protocol] Denature both the sample and input DNA in a heatblock set at 100 °C for 10 minutes. Cool down on ice.  When cold, add 2 μl of anti-Methylcytosine (5MeC) antibody (Diagenode, Cat#: MAb-006-100, Lot#: DA-0017) to sample DNA. Rotate tubes overnight at 4°C. Next day add 90 ul of Pro-A sepharose slurry (Pharmacia) to each tube. Rotate at 4 C for 1hr.  Transfer samples and beads to a Handee spin cup column with paper filter (Pierce).  Spin samples for ~10 seconds in a picofuge to remove the buffer.  Wash beads for 5 min at 4 C with 400 ul each of the following buffers:  low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA from the beads by adding 250 l of pre-warmed (60°C) QG buffer (Qiagen Quick Spin Kit). Incubate the spin column with the QG buffer in a heat block set at 100oC for 5 min. Gently vortex the samples for 5 min at RT.  Spin the sample for ~10 seconds in a picofuge and transfer the eluate to a clean 1.5 ml microfuge tube.  Repeat the elution step. Add 450 μl of prewarmed QG buffer to the input DNA, incubate for 5 minutes at 100 °C, shake for 5 min. at RT, and spin in a picofuge. Add 150 μl of isopropanol to 500 μl of eluate or diluted input. Put the samples in a QIAquick column and spin for 1 minute at maximum speed. Wash with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

value: anti-Methylcytosine (5MeC) antibody (Diagenode, Cat#:MAb-006-100, Lot#:DA-0017)

source_name: [Input DNA] DNAmet_MB453


title: 48RT_EP [H3K27me3]

source_name: [IP DNA] H3K27me3_48RT_EP

source_name: [Input DNA] H3K27me3_48RT_EP


title: BT549 [DNAmet]

description: breast carcinoma cell line

source_name: [IP DNA] DNAmet_BT549

source_name: [Input DNA] DNAmet_BT549


title: relA spoT MSP 2

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 3.0 replicate 2

value: mid stationary

source_name: SL1344 genomic DNA


title: relA spoT MSP 3

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 3.0 replicate 3


title: 48L_FB [H3K27me3]

description: Human mammary fibroblast cells

source_name: [IP DNA] H3K27me3_48L_FB

value: mammary gland

source_name: [Input DNA] H3K27me3_48L_FB


title: relA spoT MSP 1

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 3.0 replicate 1


title: relA spoT LSP 1

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 3.6 replicate 1


title: relA spoT LSP 2

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 3.6 replicate 2


title: relA spoT ESP 2

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 2.3 replicate 2

value: early stationary


title: relA spoT ESP 1

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 2.3 replicate 1


title: relA spoT ESP 3

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 2.3 replicate 3


title: relA spoT ML 2

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 1.0 replicate 2

value: mid log


title: relA spoT ML 1

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 1.0 replicate 1


title: MB231 [DNAmet]

description: breast carcinoma cell line

source_name: [IP DNA] DNAmet_MB231

value: breast carcinoma cell line

source_name: [Input DNA] DNAmet_MB231


title: WT LSP 3

source_name: SL1344 cDNA OD600 = 3.6 replicate 3

value: wild type


title: 184B [DNAmet]

source_name: [IP DNA] DNAmet_184B

source_name: [Input DNA] DNAmet_184B


title: relA spoT ML 3

source_name: SL1344 cDNA ∆relA ,∆spoT OD600 = 1.0 replicate 3

source_name: SL1344 genomic DNA


title: 48RS [DNAmet]

source_name: [IP DNA] DNAmet_48RS

source_name: [Input DNA] DNAmet_48RS


title: 184A1_21p [DNAmet]

description: Immortal human mammary epithelial cells

source_name: [IP DNA] DNAmet_184A1_21p

source_name: [Input DNA] DNAmet_184A1_21p


title: 184A1_14p [DNAmet]

description: Immortal human mammary epithelial cells

source_name: [IP DNA] DNAmet_184A1_14p

source_name: [Input DNA] DNAmet_184A1_14p


title: WT LSP 2

source_name: SL1344 cDNA OD600 = 3.6 replicate 2


title: 184A1-TERT [DNAmet]

description: Immortal human mammary epithelial cells

source_name: [IP DNA] DNAmet_184A1-TERT

source_name: [Input DNA] DNAmet_184A1-TERT


title: MCF7 [DNAmet]

description: breast carcinoma cell line

source_name: [IP DNA] DNAmet_MCF7

source_name: [Input DNA] DNAmet_MCF7


title: 240LB_EP [DNAmet]

source_name: [IP DNA] DNAmet_240LB_EP

source_name: [Input DNA] DNAmet_240LB_EP


title: 1B3.Treg.Rep2.Tech2

description:
Gene expression from sorted T cells
1B3_Toe14_Tregs

source_name: regulatory T cells from 1B3 transgenic mouse. Biological replicate 2. Technical replicate 2.

value: 1B3 transgenic

value: Sorted CD4+ regulatory T cells from spleen and lymph nodes


title: 1B3.Tconv.Rep4.Tech1

source_name: conventional T cells from 1B3 transgenic mouse. Biological replicate 4. Technical replicate 1.

value: Sorted CD4+ conventional T cells from spleen and lymph nodes


title: 184Aa_11p [DNAmet]

source_name: [IP DNA] DNAmet_184Aa_11p

value: Post-Stasis human mammary epithelial cells

source_name: [Input DNA] DNAmet_184Aa_11p


title: WT MSP 1

source_name: SL1344 cDNA OD600 = 3.0 replicate 1

source_name: SL1344 genomic DNA


title: WT LSP 1

source_name: SL1344 cDNA OD600 = 3.6 replicate 1

value: late stationary


title: WT MSP 3

source_name: SL1344 cDNA OD600 = 3.0 replicate 3


title: WT ESP 3

source_name: SL1344 cDNA OD600 = 2.3 replicate 3


title: WT MSP 2

source_name: SL1344 cDNA OD600 = 3.0 replicate 2


title: WT ESP 2

source_name: SL1344 cDNA OD600 = 2.3 replicate 2


title: WT ESP 1

source_name: SL1344 cDNA OD600 = 2.3 replicate 1


title: ProJAM1_JAM1-SRDX_Arabidopsis_11days_seedling_treated_with_JA-rep4

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description:
JAM1SRDX_JA_rep4
Many seedlings were grown in liquid medium and were harvested for RNA extraction.

hyb_protocol: Hybridized using the Gene Expression Hybridization kit (Agilent) and washed by the Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).
Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, the signal of each probe was divided by the median value of filter-passed probes.

source_name: ProJAM1:JAM1-SRDX Arabidopsis thaliana 11days seedlings treated with JA

label_protocol: 200 ng of total RNA was used for the labeling procedure using the Low Input Quick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown in MS (1% sucrose) liquid medium in a 16hr light / 8hr dark cycle in 23 Celsius degrees.

extract_protocol: The Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

treatment_protocol: MeJA in DMSO or DMSO only was added to liquid medium in a final concentration of 50 microM and cultured 1 hour.

tag: ecotype

tag: genotype

value: whole seedlings

value: jasmonate (JA)


title: WT ML 3

source_name: SL1344 cDNA OD600 = 1.0 replicate 3

tag: strain


title: 184D_EP [DNAmet]

source_name: [IP DNA] DNAmet_184D_EP

value: Pre-Stasis human mammary epithelial cells

source_name: [Input DNA] DNAmet_184D_EP


title: 172_organoid [DNAmet]

description: Human mammary organoids

source_name: [IP DNA] DNAmet_172_organoid

value: Human mammary organoids

source_name: [Input DNA] DNAmet_172_organoid


title: 48L_FB [DNAmet]

description: Human mammary fibroblast cells

source_name: [IP DNA] DNAmet_48L_FB

value: Human mammary fibroblast cells

source_name: [Input DNA] DNAmet_48L_FB


title: WT ML 2

source_name: SL1344 cDNA OD600 = 1.0 replicate 2


title: 48RT_EP [DNAmet]

source_name: [IP DNA] DNAmet_48RT_EP

value: anti-Methylcytosine (5MeC) antibody (Diagenode, Cat#:MAb-006-100, Lot#:DA-0017)

source_name: [Input DNA] DNAmet_48RT_EP


title: 184_FB [DNAmet]

description: Human mammary fibroblast cells

source_name: [IP DNA] DNAmet_184_FB

source_name: [Input DNA] DNAmet_184_FB


title: 60R_organoid [DNAmet]

description: Human mammary organoids

source_name: [IP DNA] DNAmet_60R_organoid

source_name: [Input DNA] DNAmet_60R_organoid


title: 240L_FB [DNAmet]

description: Human mammary fibroblast cells

source_name: [IP DNA] DNAmet_240L_FB

source_name: [Input DNA] DNAmet_240L_FB


title: WT ML 1

source_name: SL1344 cDNA OD600 = 1.0 replicate 1

source_name: SL1344 genomic DNA


title: ProMYC2_MYC2-SRDX_Arabidopsis_11days_seedling_treated_with_JA-rep4

description:
MYC2SRDX_JA_rep4
Many seedlings were grown in liquid medium and were harvested for RNA extraction.

source_name: ProMYC2:MYC2-SRDX Arabidopsis thaliana 11days seedlings treated with JA

tag: treatment


title: Input

city: Lausanne

first: Nicolas

last: Lonfat

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL - Ecole Polytechnique Fédérale de Lausanne

hyb_protocol: 1μg of DNA was hybridzed per array for 16 hours at 45° at 60rpm using the Affymetrix hybridization kit.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: Array data were normalized with input replicates and scaled to feature intensity of 100 using TAS software (Affymetrix). PM-MM pairs mapping within a sliding window of 250 bp was used.    Processed data: bar files of normalized signals

label: biotin

source_name: Input DNA from E12.5 mouse limbs

label_protocol: 1 ug of 4C and input DNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: 4C analysis was as described (Montavon et. al, 2011) using E12.5 digits; briefly 2% formaldehyde-fixed nuclei from collagenase-dissociated tissues were stored at −80°C before genotyping. Pools of 10 pairs of mutant digits were used for each 4C analysis using DpnII restriction enzyme to identify interacting partners of the lacZ sequence from the transgene, allowing for an allele-specific conformation capture Primers used for amplification were: lacZD2 F: GTC GTT TGC CGT CTG AAT TT and lacZD2 R: GAG GGG ACG ACG ACA GTA TC.

value: forelimb


title: 4C_INVM2_M3

source_name: Autopods Inv(Rel5-Itga6) Maternal/+ 4C from lacZ

value: autopods

tag: transgene

value: lacZ


title: 4C_INVP2_P3

source_name: Autopods Inv(Rel5-Itga6) +/Paternal 4C from lacZ

tag: age


title: Double knock-out CD71mid Ter119high erythroblasts replicate 1

city: Shanghai

first: Helen

middle: He

last: Zhu

address: 3rd Floor, Building 5, 1630 Dongfang Road

department: Stem Cell Center, Renji Hospital

country: China

institute: School of Medicine, Shanghai Jiaotong University

description:
replicate 1
SAMPLE 7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized with cubic spine using illumina genomestudio.

source_name: bone marrow

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

growth_protocol: cells are isolated freshly from mice bone marrow

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

treatment_protocol: cells are sorted by high speed flow cytometry into Trizol reagent

value: Double knock-out

value: CD71mid Ter119high erythroblasts


title: ProJAM1_JAM1-SRDX_Arabidopsis_11days_seedling_treated_with_JA-rep3

description:
JAM1SRDX_JA_rep3
Many seedlings were grown in liquid medium and were harvested for RNA extraction.

source_name: ProJAM1:JAM1-SRDX Arabidopsis thaliana 11days seedlings treated with JA

tag: tissue


title: Wild_type_Arabidopsis_11days_seedling_treated_with_JA-rep2

description:
control_JA_rep2
Many seedlings were grown in liquid medium and were harvested for RNA extraction.

source_name: Wild-type Arabidopsis thaliana 11days seedlings treated with JA

value: wt


title: Pten knock-out CD71mid Ter119high erythroblasts replicate 2

description:
replicate 2
SAMPLE 6

value: Pten knock-out


title: ProMYC2_MYC2-SRDX_Arabidopsis_11days_seedling_treated_with_JA-rep1

description:
MYC2SRDX_JA_rep1
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: ProMYC2_MYC2-SRDX_Arabidopsis_11days_seedling_treated_with_JA-rep3

description:
MYC2SRDX_JA_rep3
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: Wild_type_Arabidopsis_11days_seedling_treated_with_JA-rep4

description:
control_JA_rep4
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: Shp2 knock out CD71mid Ter119high erythroblasts replicate 1

description:
replicate 1
SAMPLE 3

value: Shp2 knock-out


title: ProJAM1_JAM1-SRDX_Arabidopsis_11days_seedling_treated_with_mock-rep3

description:
JAM1SRDX_mock_rep3
Many seedlings were grown in liquid medium and were harvested for RNA extraction.

source_name: ProJAM1:JAM1-SRDX Arabidopsis thaliana 11days seedlings treated with mock

value: mock


title: ProMYC2_MYC2-SRDX_Arabidopsis_11days_seedling_treated_with_JA-rep2

description:
MYC2SRDX_JA_rep2
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: Double knock-out CD71mid Ter119high erythroblasts replicate 2

description:
replicate 2
SAMPLE 8


title: ProJAM1_JAM1-SRDX_Arabidopsis_11days_seedling_treated_with_mock-rep4

description:
JAM1SRDX_mock_rep4
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: Shp2 knock out CD71mid Ter119high erythroblasts replicate 2

description:
replicate 2
SAMPLE 4


title: Pten knock-out CD71mid Ter119high erythroblasts replicate 1

description:
replicate 1
SAMPLE 5


title: 4C_Rel5M1

source_name: Autopods Rel5 Maternal/+ 4C from lacZ


title: Wild_type_Arabidopsis_11days_seedling_treated_with_JA-rep3

description:
control_JA_rep3
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: Wild_type_Arabidopsis_11days_seedling_treated_with_JA-rep1

description:
control_JA_rep1
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: ProJAM1_JAM1-SRDX_Arabidopsis_11days_seedling_treated_with_JA-rep1

description:
JAM1SRDX_JA_rep1
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: ProJAM1_JAM1-SRDX_Arabidopsis_11days_seedling_treated_with_JA-rep2

description:
JAM1SRDX_JA_rep2
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: Wide type CD71mid Ter119high erythroblasts replicate 1

description:
replicate 1
SAMPLE 1

value: wild type


title: ProJAM1_JAM1-SRDX_Arabidopsis_11days_seedling_treated_with_mock-rep2

description:
JAM1SRDX_mock_rep2
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: Wide type CD71mid Ter119high erythroblasts replicate 2

description:
replicate 2
SAMPLE 2


title: 4C_Rel5P1

source_name: Autopods Rel5 +/Paternal 4C from lacZ


title: ProJAM1_JAM1-SRDX_Arabidopsis_11days_seedling_treated_with_mock-rep1

description:
JAM1SRDX_mock_rep1
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: MommeD1 Female Rep4

city: Parkville

first: Matthew

middle: J

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute

description: replicate 4

source_name: E9.5 embryos

label_protocol: biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit from Applied Biosystems

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control (RIN>8) was performed with Agilent Bioanalyser.

value: FVB/n

tag: gender

value: female

tag: developmental stage

tag: ChIP


title: Wildtype Female Rep4

description: replicate 4

value: Wildtype


title: Foot 3

city: Baltimore

first: Luis

middle: Andres

last: Garza

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

description: from full thickness 3mm skin punch biopsy

hyb_protocol: Dried labeled samples were resuspended in hybridization buffer, incubated @100C for 5 min., hybridized with rotation @ 55C for 20hr., then washed as per Agilent protocol.

scan_protocol: Arrays were scanned with an Agilent G2505 scanner using Agilent's Feature Extraction software to produce Feature Extraction .txt output files under their recommended protocol.

data_processing: Feature Extraction gMedianSignal values were imported and processed with Partek Genomics Suite using quantile normalization and output in Log2 notation.

source_name: Dorsum of Foot

label_protocol: Dephosphorylated RNA samples were ligated to pCp-Cy3 label with T4 RNA ligase as per Agilent's recommended protocol.

growth_protocol: Only fresh human biopsies were used

extract_protocol: total RNA (Qiagen) extracted including miRNA

treatment_protocol: Biopsies were not treated

value: Skin from Dorsum of Foot

tag: donor #


title: Sole 4

source_name: Sole

value: Skin from Sole


title: Sole 3


title: Foot 4


title: Hand 4

source_name: Dorsum of Hand

value: Skin from Dorsum of Hand


title: Hand 3


title: Palm 4

source_name: Palm

value: Skin from Palm


title: Palm 1


title: ProMYC2_MYC2-SRDX_Arabidopsis_11days_seedling_treated_with_mock-rep4

description:
MYC2SRDX_mock_rep4
Many seedlings were grown in liquid medium and were harvested for RNA extraction.

source_name: ProMYC2:MYC2-SRDX Arabidopsis thaliana 11days seedlings treated with mock

value: whole seedlings


title: Palm 2


title: MommeD1 Female Rep3

description: replicate 3


title: 184A1_49p [DNAmet]

description: Immortal human mammary epithelial cells

source_name: [IP DNA] DNAmet_184A1_49p

value: mammary gland

value: Immortal human mammary epithelial cells

tag: chip antibody

value: anti-Methylcytosine (5MeC) antibody (Diagenode, Cat#:MAb-006-100, Lot#:DA-0017)

source_name: [Input DNA] DNAmet_184A1_49p


title: ProMYC2_MYC2-SRDX_Arabidopsis_11days_seedling_treated_with_mock-rep3

description:
MYC2SRDX_mock_rep3
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: ProMYC2_MYC2-SRDX_Arabidopsis_11days_seedling_treated_with_mock-rep2

description:
MYC2SRDX_mock_rep2
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: Sole 1


title: Hand 2


title: Wildtype Male Rep4

description: replicate 4

value: male


title: Wildtype Female Rep3

description: replicate 3


title: Palm 3


title: Wild_type_Arabidopsis_11days_seedling_treated_with_mock-rep3

description:
control_mock_rep3
Many seedlings were grown in liquid medium and were harvested for RNA extraction.

source_name: Wild-type Arabidopsis thaliana 11days seedlings treated with mock

value: wt


title: MommeD1 Male Rep4

description: replicate 4


title: Wildtype Male Rep3

description: replicate 3


title: MommeD1 Male Rep3

description: replicate 3


title: Wild_type_Arabidopsis_11days_seedling_treated_with_mock-rep2

description:
control_mock_rep2
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: Wild_type_Arabidopsis_11days_seedling_treated_with_mock-rep4

description:
control_mock_rep4
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: ProMYC2_MYC2-SRDX_Arabidopsis_11days_seedling_treated_with_mock-rep1

description:
MYC2SRDX_mock_rep1
Many seedlings were grown in liquid medium and were harvested for RNA extraction.


title: Hand 1


title: Sole 2


title: Foot 1


title: MommeD1 Female Rep2

description: replicate 2


title: Foot 2


title: Wildtype Male Rep2

description: replicate 2


title: Wildtype Female Rep2

description: replicate 2


title: Palm_rep3 (dermis)

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip® Expression Wash, Stain and Scan User Manual (www.affymetrix.com).

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Image analysis used the Affymetrix Command Console version 3 (AGCC v3.0) software, processed with the Expression Console PLIER algorithm and the manufacturer’s specifications.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na31.hg19.probeset_extended.mps

source_name: Dermis from punch biopsy

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter engineered random primers for cDNA synthesis, and Ambion® WT Expression Kit (www.affymetrix.com).

growth_protocol: after biopsy, skin was treated with dipsase to isolate epidermis. Epidermal samples were stored in RNAlater prior to RNA extraction. No growth.

extract_protocol: Qiagen Fibrous RNA kit

treatment_protocol: no treatments

tag: volar or non-volar

value: volar

tag: upper or lower extremity

value: upper


title: 6h Submerged Arabidopsis (wrky22-ko2) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

hyb_protocol: Arrays in this study were carried out with the Agilent Arabidopsis Gene Expression Microarray, V4 version 4× 44k array (Agilent, Santa Clara, CA, USA), based on the manufacturer's two-color microarray protocols.  Hybridyzation experiments were performed at the DNA Microarray Core facility, Institute of Plant and Microbial Biology, Academia Sinica, as described on http://ipmb.sinica.edu.tw/microarray/protocol.htm.

scan_protocol: Array signals were detected and analyzed using the Agilent DNA Microarray Scanner G2565CA and Agilent Feature Extraction 10.7.1.1 software, respectively.

data_processing: The acquired results were then imported into GeneSpring 11.5 (Agilent Technologies, Santa Clara, CA, USA) using LOWESS Normalization.

source_name: 6h Submerged Arabidopsis (wrky22-ko2)

label_protocol: 10 µg of total RNA were primed with 1.25 µl of 100 µM Oligo dTV DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dCTP, dGTP, with 100 µM dTTP, 400 µM aminoallyl-dUTP. The aminoallyl-labeled cDNA was hydrolyzed to obtain single stranded labeled DNA with addition of 10 µl of 0.5 M EDTA and 10 µl of 1 N NaOH at 65℃ for 15 min followed by neutralization with 25 µl of 1 M HEPES, pH 7.4.  The labed DNA was then purified with Microcon-30 concentrator by washing with water for three times.  NHS-ester Cy dyes were used to couple with the aminoally-cDNA at room temperature for 1 h.  Unreacted NHS-ester Cy dyes were quenched with addition of 4.5 µl of 4 M hydroxylamine and removed by PCR clean up kit (QIAGEN).  For details, see http://ipmb.sinica.edu.tw/microarray/protocol.htm.

growth_protocol: Experiments were carried out on Arabidopsis thaliana ecotype Columbia-0.  Two T-DNA insertion mutant lines of WRKY22, wrky22-ko1 (SALK_047120) and wrky22-ko2 (SALK_098205), were obtained from the Arabidopsis Biological Resource Center, Ohio State University, USA.  All seeds were surface-sterilized with 0.5% of sodium hypochloride for 20 minutes and washed at least five times with sterilized water.  Seeds were sown on plates with 0.55% of phytagel (Sigma-Aldrich, St. Louis, MO, USA) in half-strength MS medium (Duchefa Biochemie BV, Haarlem, Netherlands) containing 0.5% sucrose at pH 5.7, and kept at 4oC in the dark for 3 days to achieve uniform germination.  The plates were then transferred to a growth chamber and placed vertically, and plants were grown at 22ºC under a 16-hour light (81 μmol s-1 m-2)/8-hour dark cycle until 9-day-old.

extract_protocol: Total RNA was isolated from shoots or roots using TRIZOL reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacture's description using a 1:2 ratio of sample:TRIZOL reagent.  Total RNA was subjected to DNase treatment using the TURBO RNA free kit (Ambion) according to the manufacture's instructions. Genomic DNA contamination and RNA integrity were tested on an Agilent 2100 Bioanalyzer.

treatment_protocol: Plates with plants on the surface of the medium were placed into half-strength MS liquid medium that was bubbled with 3 % oxygen balanced with nitrogen for the indicated times.  The liquid MS medium was pretreated with 3% oxygen for one hour before use.

tag: genetic background

value: Columbia

value: seedling

tag: time (h)

value: submerged

source_name: Arabidopsis (wrky22-ko2) without Submergence Treatment

value: control


title: MommeD1 Male Rep2

description: replicate 2

value: FVB/n


title: MommeD1 Female Rep1

description: replicate 1

value: female


title: Hand_rep2 (dermis)

value: non-volar


title: MommeD1 Male Rep1

description: replicate 1


title: 6h Submerged Arabidopsis (wrky22-ko2) Replicate 1

description: Biological replicate 1 of 4.


title: 6h Submerged Arabidopsis (wrky22-ko2) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Wildtype Female Rep1

description: replicate 1

value: Wildtype


title: Sole_rep3 (dermis)

value: lower


title: Hand_rep3 (dermis)


title: Sole_rep2 (dermis)


title: 6h Submerged Arabidopsis (wrky22-ko2) Replicate 3

description: Biological replicate 3 of 4.


title: Palm_rep2 (dermis)


title: Wildtype Male Rep1

description: replicate 1


title: Foot_rep2 (dermis)


title: Sole_rep1 (dermis)


title: 3h Submerged Arabidopsis (wrky22-ko2) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

source_name: 3h Submerged Arabidopsis (wrky22-ko2)


title: Foot_rep3 (dermis)


title: Hand_rep1 (dermis)


title: Foot_rep1 (dermis)


title: Palm_rep1 (dermis)


title: Nrl replicate-5

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

hyb_protocol: Samples were hybridized to Illumina mouse ref-8 version 2 microarrays and processed according to manufactgurer's directions.

scan_protocol: Microarrays were scanned on an Illumina iScan scanner.

data_processing: Data from the scanner was obtained with GenomeStudio software (Illumina) and quantile normalized (Matlab).

source_name: retina

label_protocol: RNA samples were labeled using Illumina Total Prep RNA Amplification Kit according to the manufacturer’s directions

growth_protocol: Samples were obtained from CNGA3-/-/Nrl-/-, CNGB3-/-/Nrl-/-, and Nrl-/- mouse retinas

extract_protocol: Retinas from each animal were pooled and stored in Trizol. Five mice at postnatal 30 days were used in each group.  At the time of extraction, the retinas were homogenized and total RNA was isolated using a PureLinkTM RNA Mini Kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions.

value: Nrl-/-

value: postnatal day 30

value: retina


title: 3h Submerged Arabidopsis (wrky22-ko2) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: 3h Submerged Arabidopsis (wrky22-ko2) Replicate 3

description: Biological replicate 3 of 4.


title: Sole_rep1 (basal)

source_name: Sorted basal layer keratinocytes from epidermis of punch biopsy

growth_protocol: after biopsy, skin was treated with dipsase to isolate epidermis. Epidermis was trypsinized, and keratinocytes were sorted according to viabilility and alpha 6 integrin positivity. Keratinocytes were stored in RNAlater prior to RNA extraction. No growth.

extract_protocol: Qiagen  RNAeasy kit


title: volar epidermis from Sole rep3

data_processing:
Image analysis used the Affymetrix Command Console version 3 (AGCC v3.0) software, processed with the Expression Console PLIER algorithm and the manufacturer’s specifications.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.na31.hg19.probeset_extended.mps

source_name: Epidermis from punch biopsy

value: volar epidermis from Sole


title: Wild_type_Arabidopsis_11days_seedling_treated_with_mock-rep1

description:
control_mock_rep1
Many seedlings were grown in liquid medium and were harvested for RNA extraction.

value: whole seedlings

value: mock


title: Foot_rep1 (basal)


title: 3h Submerged Arabidopsis (wrky22-ko2) Replicate 1

description: Biological replicate 1 of 4.


title: Nrl replicate-4


title: volar epidermis from Palm rep3

value: volar

value: volar epidermis from Palm


title: Nrl replicate-3


title: CNGB3 replicate-4


title: Sole_rep2 (basal)


title: 1h Submerged Arabidopsis (wrky22-ko2) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

source_name: 1h Submerged Arabidopsis (wrky22-ko2)

value: Columbia


title: non-volar epidermis from Hand rep3

value: upper

value: non-volar epidermis from Hand


title: non-volar epidermis from Foot rep3

value: non-volar epidermis from Foot


title: volar epidermis from Sole rep2


title: 1h Submerged Arabidopsis (wrky22-ko2) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.

value: seedling

value: submerged

value: control


title: volar epidermis from Palm rep2


title: non-volar epidermis from Hand rep2

value: non-volar


title: 1h Submerged Arabidopsis (wrky22-ko2) Replicate 1

description: Biological replicate 1 of 4.


title: Foot_rep2 (basal)

value: lower


title: CNGB3 replicate-5


title: CNGA3 replicate-4


title: CNGA3 replicate-5


title: 1h Submerged Arabidopsis (wrky22-ko2) Replicate 3

description: Biological replicate 3 of 4.


title: non-volar epidermis from Foot rep2


title: Nrl replicate-2

value: Nrl-/-


title: 6h Submerged Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.

source_name: 6h Submerged Arabidopsis (Columbia)

value: wt

source_name: Arabidopsis (Columbia) without Submergence Treatment


title: volar epidermis from Sole rep1


title: volar fibroblast from Sole rep3

source_name: Dermal fibroblasts expanded from punch biopsy

tag: cell type

value: volar fibroblast from Sole


title: non-volar epidermis from Hand rep1


title: 6h Submerged Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: volar epidermis from Palm rep1


title: CNGA3 replicate-3

value: postnatal day 30

value: retina


title: CNGB3 replicate-2


title: volar fibroblast from Sole rep2


title: CNGB3 replicate-1


title: volar fibroblast from Palm rep3

value: volar fibroblast from Palm


title: 6h Submerged Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: non-volar fibroblast from Hand rep2

value: non-volar fibroblast from Hand


title: non-volar fibroblast from Foot rep3

value: non-volar fibroblast from Foot


title: non-volar epidermis from Foot rep1


title: 6h Submerged Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.

value: Columbia


title: non-volar fibroblast from Hand rep3

value: upper


title: CNGB3 replicate-3


title: 3h Submerged Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

source_name: 3h Submerged Arabidopsis (Columbia)


title: volar fibroblast from Palm rep1

value: volar


title: non-volar fibroblast from Foot rep2


title: non-volar fibroblast from Hand rep1


title: CNGA3 replicate-2


title: 3h Submerged Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.


title: volar fibroblast from Sole rep1


title: 3h Submerged Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: 3h Submerged Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.


title: Cj1000_Bio3_Tech3_Column3

city: Ottawa

first: Alain

last: Stintzi

state: Ontario

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Ottawa

description: biological replicate 3 of 3, technical replicate 9 of 9

hyb_protocol: Fluorescently labelled cDNA samples from the wild type C. jejuni reference strain and the cj1000::aph mutant strain were combined, vacuum dried, and resuspended in 36µl of hybridization buffer (5X SSC, 25% formamide, 0.1% SDS, and 25µg salmon sperm DNA). NCTC11168 microarray slides were prepared for hybridization by incubation in slide hybridization buffer (5X SSC, 25% formamide, 0.1% SDS, and 1% BSA) for 45 minutes at 42°C. The fluorescently labelled, pooled cDNA samples were hybridized to the microarray slide a under glass coverslip which was placed in a humidified chamber (ArrayIt) overnight at 42°C protected from light. Following overnight incubation, the microarray slide was washed in 100mL of 2X SSC, 0.1% SDS solution for 5 min at 42°C. The slide was subsequently washed in 100mL of 0.1X SSC, 0.1% SDS at room temperature for 10 min and followed by an additional 4x 1 min washes in 0.1X SSC, 0.1% SDS solution. The slide was rinsed briefly in distilled H2O and dried by centrifugation.

scan_protocol: Microarray slides were scanned at 532 nm (Cy3) and 635 nm (Cy5) wavelengths using a laser-activated confocal scanner (ScanArray Gx, Perkin Elmer) at a 10µm resolution.

data_processing: Data collection was performed using the ScanArray software (Perkin Elmer) which determines the signal intensity for each spot on the microarray. Spots that were localized within regions of hybridization abnormalities were removed from the analysis and the raw fluorescent intensities for each spot were subtracted from the background fluorescence of the microarray. Spots that had background-subtracted intensity values less than three times the standard deviation of the local background in both Cy3 and Cy5 channels were subsequently removed from data analysis. Next, MIDAS software (available from TIGR; http://www.tigr.org/software/) was used along with locally weighted linear regression (Lowess) to normalize the fluorescent intensity values. The ratio of the fluorescent intensity values in the Cy3 channel to the Cy5 channel was calculated and converted into a log2 value.

organism: Campylobacter jejuni

source_name: NCTC11168 wild-type

label_protocol: Preparation of fluorescently labelled cDNA and microarray slide hybridization was performed as described previously (Palyada et al., 2004). Briefly, 16µg of wild type C. jejuni or cj1000::aph extracted RNA was reversed transcribed in presence of 10µg random hexamers, 0.5mM dGTP, dATP, dCTP, 0.16mM dTTP, and 0.34mM aminoallyl dUTP using SuperScript II (Invitrogen) for 2 hours at 42°C. The reaction was stopped by the addition of 50mM EDTA and 10 N NaOH and incubated at 65°C for 20 minutes. The reaction was neutralized by addition of 5M acetic acid and the aminoallyl-labelled cDNA was purified from non-incorporated aminoallyl dUTPs using Micron YM-30 spin columns (Millipore). The purified aminoallyl-labelled cDNA was coupled to Cy3 or Cy5 monoreactive fluors (Amersham) using the method described previously (Palyada et al., 2004). Following the coupling of fluorescent dyes to cDNA, the cDNA samples were purified using the PureLink PCR Purification Kit (Invitrogen) according to the manufacturer’s specifications.

growth_protocol: C. jejuni NCTC11168 wild-type and Cj1000 mutant strains were incubed in 100 ml flasks containing 25 ml of MEMα medium plus 20 mM sodium pyruvate, at 37°C under microaerobic conditions, with stirring. Cells were grown to mid-log phase before total RNA extraction.

extract_protocol: At mid-log phase (OD600 of 0.2),  2.5mL cold RNA degradation stop solution (10% buffer-saturated phenol pH 4.3 in ethanol) were added to prevent RNA decay. Bacterial cells were harvested by centrifugation, resuspended in TE buffer followed by total RNA isolation using the hot phenol-chloroform method. Extracted RNA samples were treated twice with DNase-I (Epicenter) and purified using the RNeasy kit (Qiagen) followed by PCR amplification to confirm the absence of contaminating genomic DNA in the samples. The Experion RNA STDsens Analysis Kit (Bio-Rad Laboratories) was used to quantify and confirm RNA integrity of the extracted RNA samples. RNA samples were stored at -80°C.

tag: background strain

tag: genotype/variation

value: wild-type

source_name: NCTC11168 Cj1000 mutant


title: Nrl replicate-1

tag: genotype


title: Cj1000_Bio3_Tech3_Column1

description: biological replicate 3 of 3, technical replicate 7 of 9


title: Cj1000_Bio3_Tech3_Column2

description: biological replicate 3 of 3, technical replicate 8 of 9


title: Cj1000_Bio3_Tech2_Column3

description: biological replicate 3 of 3, technical replicate 6 of 9


title: non-volar fibroblast from Foot rep1


title: 1h Submerged Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

source_name: 1h Submerged Arabidopsis (Columbia)

value: seedling

tag: treatment


title: 1h Submerged Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.

value: submerged


title: Cj1000_Bio2_Tech3_Column3

description: biological replicate 2 of 3, technical replicate 9 of 9


title: Cj1000_Bio3_Tech2_Column1

description: biological replicate 3 of 3, technical replicate 4 of 9


title: Cj1000_Bio3_Tech1_Column2

description: biological replicate 3 of 3, technical replicate 2 of 9


title: Cj1000_Bio3_Tech1_Column3

description: biological replicate 3 of 3, technical replicate 3 of 9


title: CNGA3 replicate-1


title: 30189376_thymus_Hmgn5_rep3

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: replicate 3

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

value: male

value: Hmgn5 mutant

value: 17 weeks

tag: mouse id

value: thymus


title: 30189375_thymus_Hmgn5_rep4

description: replicate 4

tag: age

tag: tissue


title: 1h Submerged Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.

value: wt

value: control


title: 30189372_thymus_Hmgn5_rep1

description: replicate 1

tag: gender


title: Cj1000_Bio3_Tech2_Column2

description: biological replicate 3 of 3, technical replicate 5 of 9


title: Cj1000_Bio2_Tech3_Column1

description: biological replicate 2 of 3, technical replicate 7 of 9


title: Cj1000_Bio2_Tech2_Column1

description: biological replicate 2 of 3, technical replicate 4 of 9


title: Cj1000_Bio2_Tech2_Column3

description: biological replicate 2 of 3, technical replicate 6 of 9


title: Cj1000_Bio2_Tech2_Column2

description: biological replicate 2 of 3, technical replicate 5 of 9


title: Cj1000_Bio2_Tech1_Column3

description: biological replicate 2 of 3, technical replicate 3 of 9


title: Cj1000_Bio2_Tech1_Column2

description: biological replicate 2 of 3, technical replicate 2 of 9


title: Cj1000_Bio3_Tech1_Column1

description: biological replicate 3 of 3, technical replicate 1 of 9


title: Cj1000_Bio2_Tech1_Column1

description: biological replicate 2 of 3, technical replicate 1 of 9


title: Cj1000_Bio1_Tech1_Column3

description: biological replicate 1 of 3, technical replicate 3 of 3


title: Cj1000_Bio1_Tech1_Column1

description: biological replicate 1 of 3, technical replicate 1 of 3


title: Cj1000_Bio2_Tech3_Column2

description: biological replicate 2 of 3, technical replicate 8 of 9


title: 30193974_thymus_wt_rep3

description: replicate 3

value: wild type


title: 1h Submerged Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: 30189371_thymus_Hmgn5_rep2

description: replicate 2


title: Cj1000_Bio1_Tech1_Column2

description: biological replicate 1 of 3, technical replicate 2 of 3


title: 30189377_thymus_wt_rep2

description: replicate 2


title: 30189373_thymus_wt_rep4

description: replicate 4


title: 30189376_spleen_Hmgn5_rep3

description: replicate 3

value: spleen


title: 30189375_spleen_Hmgn5_rep4

description: replicate 4


title: 30189380_thymus_wt_rep1

description: replicate 1


title: bERKO Granulosa hCG biological rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression data from  bERKO granulosa cells treated for 48h with PMSG followed by 4h with hCG

hyb_protocol: 5 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 18 hours at 45°C in a rotating hybridization. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0004.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).

source_name: PMSG/hCG treated granulosa cells from bERKO mice

label_protocol: Twenty five (25) ng of total RNA was amplified as directed in the NuGEN Ovation Pico WTA System protocol, and labeled using the NuGEN Encore Biotin Module.

growth_protocol: Granulosa cells were collected from antral follicles of 3 week old WT or bERKO mice using laser micro dissection. Mice were treated with either PMSG or PMSG+hCG

extract_protocol: Total RNA was extracted using PicoPure RNA Isolation Kit (Arcturus) according to the manufacturer's instructions

treatment_protocol: Cells were collected on to LCM caps. 50 ul of Extraction buffer was added, tubes were spun and samples frozen at -80C until extraction.

value: preovulatory granulosa cells

value: 48h after PMSG + 4 h after hCG

value: bERKO


title: 30189372_spleen_Hmgn5_rep1

description: replicate 1


title: 30189371_spleen_Hmgn5_rep2

description: replicate 2


title: 30193974_spleen_wt_rep3

description: replicate 3


title: bERKO Granulosa hCG biological rep3


title: Foot3

description:
Sample name: Foot_drosum_06
from full thickness 3mm skin punch biopsy

hyb_protocol: Per Infinium chip instructions using the BeadChip Kit (WG-311-1202)

scan_protocol: performed using the Illumina iScan protocol

data_processing:
GenomeStudio v1.0 with Methylation status of each CpG site calculated as a Beta value
Matrix signal intensities value definition: Unmethylated and methylated signal intensities [linked as supplementary file on Series record]

label: Alexa555 (green) and Alexa647(red)

source_name: Dorsum of Foot

label_protocol: EZ DNA Methylation kit from Zymo Research was used for Sodium Bisulvate Conversion. Standard Illumina Protocol for labeling.

extract_protocol: Qiagen DNAeasy

tag: punch biopsy from skin site

value: Dorsum of Foot


title: 30189377_spleen_wt_rep2

description: replicate 2


title: 30189373_spleen_wt_rep4

description: replicate 4


title: bERKO Granulosa hCG biological rep1


title: WT Granulosa hCG biological rep3

description: Gene expression data from WT granulosa cells treated for 48h with PMSG followed by 4h with hCG

source_name: PMSG/hCG treated granulosa cells from WT mice

value: WT


title: Palm3

description:
Sample name: Hand_palm_06
from full thickness 3mm skin punch biopsy

source_name: Palm

tag: donor #

value: Palm


title: 30189380_spleen_wt_rep1

description: replicate 1


title: Sole3

description:
Sample name: Foot_sole_06
from full thickness 3mm skin punch biopsy

source_name: Sole

value: Sole


title: Hand3

description:
Sample name: Hand_dorsum_06
from full thickness 3mm skin punch biopsy

source_name: Dorsum of Hand

value: Dorsum of Hand


title: WT Granulosa hCG biological rep1


title: WT Granulosa hCG biological rep2


title: Sole2

description:
Sample name: Foot_sole_05
from full thickness 3mm skin punch biopsy


title: bERKO Granulosa PMSG biological rep3

description: Gene expression data from bERKO granulosa cells treated for 48h with PMSG

source_name: PMSG treated granulosa cells from bERKO mice

value: 48h after PMSG


title: 30189376_liver_Hmgn5_rep3

description: replicate 3

value: male

value: liver


title: Hand2

description:
Sample name: Hand_dorsum_05
from full thickness 3mm skin punch biopsy


title: bERKO Granulosa PMSG biological rep2


title: 30189375_liver_Hmgn5_rep4

description: replicate 4

value: Hmgn5 mutant

value: 17 weeks


title: 30189371_liver_Hmgn5_rep2

description: replicate 2


title: WT Granulosa PMSG biological rep3

description: Gene expression data from WT granulosa cells treated for 48h with PMSG

source_name: PMSG treated granulosa cells from WT mice


title: 30189372_liver_Hmgn5_rep1

description: replicate 1


title: Sole1

description:
Sample name: Foot_Sole
from full thickness 3mm skin punch biopsy


title: bERKO Granulosa PMSG biological rep1


title: Foot1

description:
Sample name: Foot Dorsum
from full thickness 3mm skin punch biopsy


title: 30189377_liver_wt_rep2

description: replicate 2


title: WT Granulosa PMSG biological rep2


title: Foot2

description:
Sample name: Foot_drosum_05
from full thickness 3mm skin punch biopsy


title: 30189371_brain_Hmgn5_rep2

description: replicate 2

value: brain


title: 30189373_liver_wt_rep3

description: replicate 3


title: WT Granulosa PMSG biological rep1


title: Palm1

description:
Sample name: Palm
from full thickness 3mm skin punch biopsy


title: Palm2

description:
Sample name: Hand_palm_05
from full thickness 3mm skin punch biopsy


title: Hand1

description:
Sample name: Dorsum_Hand
from full thickness 3mm skin punch biopsy


title: wdNHBE uninfected at 36hpi, biological rep2

city: Louisville

first: Rachael

last: Gerlach

state: KY

address: 505 S Hancock, CTR 626

department: Microbiology and Immunology

institute: University of Louisville

description: Gene expression data from well-differentiated primary human lung bronchial epithelial cells un-infected

hyb_protocol: Following fragmentation, 12.5ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human (HG_U133 plus 2.0) Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: Scanning of chip using Affymetrix Command Console (version 3.1)

data_processing: Prior to statistical analyses, raw data were processed by Plier Workflow normalization method using Gene Console software (Affymetrix, version 1.3.1).

source_name: Well-differentiated human lung epithelial cells, un-infected for 36h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Gene Chip 3' IVT Expression Kit User Manual, 2008, Affymetrix).

growth_protocol: well-differentiated cells (wd-NHBE) were purchased from MatTek Corporation (EpiAirway PC-12, Ashland, MA). Cells were maintained by incubating the 12-well formatted transwell inserts at the air-liquid interface at 37°C under 5% CO2.  The basal surface was submerged in AIR 100 (MatTek) complete growth media, made up of DMEM , epidermal growth factors, 5 µg/ml gentamicin, 0.25 µg/ml amphotericin B, and phenol red, and was replaced every 24 h until used for experiments.

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

treatment_protocol: Infection of wd-NHBE cells were conducted in serum-free growth media provided by manufacturer (MatTek).  Wd-NHBE cells, cultured at the air-liquid interface, were washed two times with Dulbecco’s phosphate buffered saline (DPBS) to remove mucus accumulation.  Virus stocks were diluted in DPBS and cells were infected at a multiplicity of infection (MOI) of 3.0 for 1 h at 37°C, 5% CO2.  Cells were washed twice with DPBS to remove unbound virus.  Basal medium was removed and replaced with complete medium.  Over the time course of infection, the basal media was removed and apical layer washed twice with DPBS supplemented with 0.2% BSA (Sigma) and stored at -80 degrees celcius until use.

tag: infection

value: Un-infected control

value: cultured primary human lung epithelial cells


title: wdNHBE uninfected at 36hpi, biological rep3


title: 30189372_brain_Hmgn5_rep1

description: replicate 1


title: 30189373_brain_wt_rep4

description: replicate 4

value: wild type


title: 30189380_liver_wt_rep1

description: replicate 1


title: 30189376_brain_Hmgn5_rep3

description: replicate 3


title: 30189377_brain_wt_rep2

description: replicate 2


title: wdNHBE uninfected at 36hpi, biological rep1


title: 30193974_brain_wt_rep3

description: replicate 3


title: wdNHBE with KY/180 at 36hpi, biological rep3

description: Gene expression data from well-differentiated primary human lung bronchial epithelial cells infected with H1N1

source_name: Well-differentiated human lung epithelial cells, infected with KY/180 (pdmH1N1) for 36h

value: 2009 pandemic H1N1 Influenza virus


title: wdNHBE with KY/180 at 36hpi, biological rep1


title: 30189380_brain_wt_rep1

description: replicate 1


title: 30184787_thymus_Hmgn3_rep4

description: replicate 4

value: Hmgn3 mutant

value: thymus


title: wdNHBE with KY/180 at 36hpi, biological rep2


title: 30184791_thymus_Hmgn3_rep2

description: replicate 2


title: wdNHBE with KY/136 at 36hpi, biological rep1

source_name: Well-differentiated human lung epithelial cells, infected with KY/136 (pdmH1N1) for 36h


title: wdNHBE with KY/136 at 36hpi, biological rep3


title: wdNHBE with BN/59 at 36hpi, biological rep1

source_name: Well-differentiated human lung epithelial cells, infected with BN/59 (seasonal H1N1) for 36h

value: seasaonal H1N1 Influenza virus


title: wdNHBE with BN/59 at 36hpi, biological rep2


title: 30184786_thymus_Hmgn3_rep3

description: replicate 3


title: 30184788_thymus_wt_rep4

description: replicate 4


title: wdNHBE with BN/59 at 36hpi, biological rep3


title: 30184789_thymus_Hmgn3_rep1

description: replicate 1


title: wdNHBE with KY/136 at 36hpi, biological rep2


title: 30184793_thymus_wt_rep2

description: replicate 2


title: 30184790_thymus_wt_rep3

description: replicate 3


title: 30184787_spleen_Hmgn3_rep4

description: replicate 4

value: spleen


title: 30184792_thymus_wt_rep1

description: replicate 1


title: sample 10_PAD_00102

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description:
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing:
Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.

source_name: White blood human cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns

treatment_protocol: White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).

tag: disease

value: pediatric acute leukemia

tag: groups

value: patient 1 (patient with new MLLT10 fusion)

tag: mrd

value: Standard Risk

tag: data analysis protocol


title: 30184789_spleen_Hmgn3_rep1

description: replicate 1


title: 30184786_spleen_Hmgn3_rep3

description: replicate 3


title: sample 8_ES_00115

value: otherHOXA

value: High Risk

value: ES


title: sample 6_PAD_00427


title: sample 11_ES_00143

value: patient 2 (patient with new MLLT10 fusion)


title: sample 9_ES_00119


title: 30184788_spleen_wt_rep4

description: replicate 4

value: male

value: 17 weeks


title: sample 7_ES_00132


title: sample 5_PAD_00402


title: 30184791_spleen_Hmgn3_rep2

description: replicate 2


title: sample 4_PAD_00387


title: sample 2_PAD_00257


title: 30184787_liver_Hmgn3_rep4

description: replicate 4

value: liver


title: 30184792_spleen_wt_rep1

description: replicate 1


title: 30184790_spleen_wt_rep3

description: replicate 3


title: 30184793_spleen_wt_rep2

description: replicate 2


title: 30184788_liver_wt_rep4

description: replicate 4


title: 30184786_liver_Hmgn3_rep3

description: replicate 3


title: 30184791_liver_Hmgn3_rep2

description: replicate 2


title: T4_Control.rep3

hyb_protocol: Hybridization protocol was performed by the Genome Core of the J. David Gladstone Institutes according to the manufacturer's instructions.

scan_protocol: Scanning protocol was performed by the Genome Core of the J. David Gladstone Institutes according to the manufacturer's instructions.

data_processing: RMA normalization

source_name: naïve T cells from blood

label_protocol: Labeling protocol was performed by the Genome Core of the J. David Gladstone Institutes according to the manufacturer's instructions.

growth_protocol: Human naïve CD4+ T cells were isolated by FACS sorter and seeded into a 12-well plates at a density of 1x10^6 cells per ml of RMPI-1640 supplemented with 5% human heat-inactivated pooled AB serum.

treatment_protocol: The cells were activated with latex beads conjugates to control antibody or antibodies specific for anti-CD3 or to both anti-CD3 and anti-CD28.

value: blood

tag: cell type

value: CD4+CD45RA+ T cells

value: Control

tag: treatment time

value: 4 hours


title: T4_CD3CD28.rep3

value: anti-CD3 + anti-CD28


title: T4_CD3CD28.rep2


title: 30184789_liver_Hmgn3_rep1

description: replicate 1

tag: genotype/variation

value: Hmgn3 mutant


title: sample 3_PAD_00115


title: T4_CD3.rep3


title: T4_CD3.rep2


title: sample 1_PAD_00117


title: 30184790_liver_wt_rep3

description: replicate 3

value: wild type


title: T4_Control.rep2


title: T4_CD3.rep1


title: 30184787_brain_Hmgn3_rep4

description: replicate 4

value: brain


title: 30184792_liver_wt_rep1

description: replicate 1


title: T24_CD3CD28.rep3

value: 24 hours


title: T4_Control.rep1


title: 30184786_brain_Hmgn3_rep3

description: replicate 3


title: 30184793_liver_wt_rep2

description: replicate 2


title: T4_CD3CD28.rep1


title: 30184791_brain_Hmgn3_rep2

description: replicate 2


title: 30184792_brain_wt_rep1

description: replicate 1


title: T24_Control.rep3


title: 30184789_brain_Hmgn3_rep1

description: replicate 1


title: T0_Control.rep3

value: 0 hours


title: 30184788_brain_wt_rep4

description: replicate 4


title: T24_CD3.rep3


title: 30184790_brain_wt_rep3

description: replicate 3


title: T0_Control.rep2


title: T24_CD3CD28.rep2


title: 30184793_brain_wt_rep2

description: replicate 2


title: T24_Control.rep2


title: 30180627_thymus_Hmgn1_rep3

description: replicate 3

value: Hmgn1 mutant

value: thymus


title: T24_CD3.rep2


title: T24_CD3.rep1


title: T24_Control.rep1


title: 30180623_thymus_Hmgn1_rep1

description: replicate 1


title: 30189375_brain_Hmgn5_rep4

description: replicate 4

value: Hmgn5 mutant


title: 30180620_thymus_Hmgn1_rep2

description: replicate 2


title: T24_CD3CD28.rep1


title: 30180625_thymus_Hmgn1_rep4

description: replicate 4


title: 30180625_spleen_Hmgn1_rep4

description: replicate 4

value: spleen


title: 30180626_thymus_wt_rep4

description: replicate 4

value: male


title: 30180624_thymus_wt_rep1

description: replicate 1

value: 17 weeks


title: 30180620_spleen_Hmgn1_rep2

description: replicate 2


title: 24-PHK HPMPC c

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450  (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.

source_name: PHK cells, 72h growth + 50µg/ml cidofovir

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: cultured at 37°C, 5% CO2 in Keratinocyte Serum Free medium

extract_protocol: 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)

treatment_protocol: attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir

value: primary human keratinocytes

value: neonatal foreskin


title: 30180621_thymus_wt_rep2

description: replicate 2


title: 30180626_spleen_wt_rep4

description: replicate 4


title: 3-HeLa control c

source_name: HeLa cells, 72h growth

growth_protocol: cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES

treatment_protocol: attached cells (24 h after passaging), grown for 72 h in renewed medium

tag: organ

value: cervix

value: adenocarcinoma

value: epithelial

tag: cell line

value: HeLa


title: 21-PHK control c

source_name: PHK cells, 72h growth


title: 6-HeLa HPMPC c

source_name: HeLa cells, 72h growth + 50µg/ml cidofovir


title: 30180623_spleen_Hmgn1_rep1

description: replicate 1

tag: strain


title: 30180622_spleen_wt_rep3

description: replicate 3

tag: mouse id


title: 30180622_thymus_wt_rep3

description: replicate 3

tag: age


title: 30180624_spleen_wt_rep1

description: replicate 1

tag: tissue


title: 30180627_spleen_Hmgn1_rep3

description: replicate 3

tag: gender


title: 18-HaCaT 51 c

source_name: HaCaT cells cidofovir resistant (#51), 72h growth

value: skin

value: keratinocyte

tag: description

value: in vitro spontaneously transformed

value: HaCaT


title: 15-HaCaT HPMPC c

source_name: HaCaT cells, 72h growth + 50µg/ml cidofovir


title: 30180621_spleen_wt_rep2

description: replicate 2

value: wild type


title: 23-PHK HPMPC b


title: 12-HaCaT control c

source_name: HaCaT cells, 72h growth


title: 17-HaCaT 51


title: 9-HeLa 52 c

source_name: HeLa cells cidofovir resistant (#52), 72h growth


title: Huh7-pNeo1

city: Dallas

first: Qiuyue

last: Chen

state: TX

address: 5323 Harry Hines Blvd.

department: Molecular Genetics

institute: UT Southwestern Medical Center

description: subclones of Huh7 cells non-permissive for HCV replication

hyb_protocol: Labeled samples were hybridized at 42˚C for 16-20h.

scan_protocol: Arrays were scaned using the MS 200 Microarray Scanner and the MS 200 Data Collection Software

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan DNA methylation data extraction.

source_name: MeDIP DNA from Huh7-pNeo1

label_protocol: 1 µg IP DNA was directly labeled by Klenow random priming with Cy5 and input DNA was labeled with Cy3 using a NimbleGen Dual-Color DNA Labeling Kit.

growth_protocol: cells were maintained in DMEM(HG) with 10% FCS and penicillin and streptomycin

extract_protocol: Genomic DNA was purified using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's protocol

treatment_protocol: Huh7-pNeo1 cells are established cell line

tag: medip antibody

tag: medip antibody vendor

value: Diagenode

tag: medip antibody lot#

tag: medip antibody catalog#

source_name: input DNA from Huh7-pNeo1

tag: antibody

value: none (input DNA)


title: HRP4

description: subclones of Huh7 cells permissive for HCV replication

source_name: MeDIP DNA from HRP4

treatment_protocol: HRP4 cells are established cell line

source_name: input DNA from HRP4


title: 30180627_liver_Hmgn1_rep3

description: replicate 3

value: Hmgn1 mutant

value: liver


title: 30180620_liver_Hmgn1_rep2

description: replicate 2

value: male


title: HRP1-2

source_name: MeDIP DNA from HRP1, replicate 2

treatment_protocol: HRP1 cells are established cell line

source_name: input DNA from HRP1


title: 11-HaCaT control b


title: 5-HeLa HPMPC b

tag: disease


title: 30180627_brain_Hmgn1_rep3

description: replicate 3

value: 17 weeks

value: brain


title: 30180625_liver_Hmgn1_rep4

description: replicate 4


title: 30180622_liver_wt_rep2

description: replicate 2


title: 30180625_brain_Hmgn1_rep4

description: replicate 4


title: 14-HaCaT HPMPC b

tag: cell type


title: 30180623_liver_Hmgn1_rep1

description: replicate 1


title: 20-PHK control b

value: primary human keratinocytes

value: neonatal foreskin


title: HRP1-1

source_name: MeDIP DNA from HRP1, replicate 1


title: 8-HeLa 52 b

value: cervix

value: adenocarcinoma


title: Huh7-pNeo2

source_name: MeDIP DNA from Huh7-pNeo2

treatment_protocol: Huh7-pNeo2 cells are established cell line

source_name: input DNA from Huh7-pNeo2


title: 16-HaCaT 51 a


title: 13-HaCaT HPMPC a


title: 19-PHK control a


title: 10-HaCaT control a


title: 30180626_liver_wt_rep3

description: replicate 3


title: 30180620_brain_Hmgn1_rep2

description: replicate 2