title: Pol II_100min_rep1

first: Sarah

last: Bray

institute: University  of Cambridge

scan_protocol: Arrays were scanned on an Axon 4000B scanner per the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. Quantile normalization was applied to the 3 arrays at each of the 7 time points.

source_name: Pol II ChIP DNA after 100 min. Notch activation

growth_protocol: DmD8 cells were cultured in Schneiders medium (Invitrogen) supplemented with 10% FBS (Sigma), 5ug/ml insulin (Sigma) and 5% penicillin / streptomycin (Sigma) according to standard protocols.

extract_protocol: Chromatin was crosslinked by fixing cells for 10 minutes with 1% formaldehyde (Sigma) at room temperature before addition of Glycine (Sigma) (0.2M final concentration) to stop the crosslinking reaction.  Cells were then detached from plates and washed twice with PBS, keeping samples at 4°C at all times.  Chromatin was released from cells by incubation with nuclear lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS, 1X complete protease inhibitor (Roche)) for 10 minutes on ice.  Crosslinked chromatin was fragmented by sonication to an average length of roughly 500bp.  Chromatin was then precleared by addition of rabbit IgG and protein G agarose beads (Santa Cruz Biotechnology) in IP dilution buffer (IPDB) (20mM Tris-HCl pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS, 1X complete protease inhibitor (Roche)) and incubation at 4°C for 5 hours with gentle agitation.  1µg Pol II (Ser 2 or Ser 5 phosphorylated) antibody (Abcam cat. no. ab5408) per sample was preincubated with protein G agarose beads in IPDB for 5 hours at 4°C with gentle agitation.  Precleared chromatin was precipitated by addition of protein G agarose beads with prebound Pol II (Ser 2 or Ser 5 phosphorylated) antibody and incubation at 4°C overnight with gentle agitation.  Beads with chromatin bound were washed twice with wash buffer 1 (20mM Tris-HCl pH 8.1, 50mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), twice with wash buffer 2 (10mM Tris-HCl pH 8.1, 250mM LiCl, 1mM EDTA, 1% NP-40, 1% deoxycholic acid) and once with TE pH 8.0.  Chromatin was then eluted from the agarose beads by incubation with elution buffer (100mM NaHCO3, 1% SDS) for 10 minutes with vigorous shaking before decrosslinking (of precipitated samples and total input) by incubating at 65°C for 5 hours with NaCl (0.27M final concentration).  Remaining proteins were removed by incubating with proteinase-K at 55°C overnight.  DNA was then purified by phenol/chloroform extraction and ethanol precipitation. Binding relative to input was quantified by qPCR.  For array analysis, DNA fragments and total input samples were amplified by ligation mediated PCR and labelled before hybridisation to tiling arrays.

tag: cell line

value: Notch stimulation

value: 100 min

value: Pol II (Ser 2 and Ser 5 phosphorylated) antibody

value: Abcam

tag: antibody catalog #

source_name: Total input after 100 min. Notch activation


title: HeDiPig_F6

status: Public on Dec 31 2012

type: RNA

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from teat tissue of peripubertal pigs of commercial dam lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing:
Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.
by PLIER algorithm

label: biotin

molecule: total RNA

organism: Sus scrofa

source_name: milk line from fetus taken at 91 day post conception

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: tissue

value: nipple

tag: breed

value: German landrace

tag: developmental stage

value: 91 dpc


title: RpoD binding site identification experiment 1

type: genomic

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Dr.

country: USA

institute: University of California, San Diego

description: ChIP-chip for RpoD binding site identification in Klebsiella pneumoniae MGH 78578

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

source_name: RpoD ChIP DNA

label_protocol: Labling was done according to manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells were cultured to mid-log phase (OD~0.6) in glucose M9 minimal media

extract_protocol: Cells were grown in 2 g/L glucose M9 minimal media at 37  C. When the cultures reached an appropriate OD, the cells were cross-linked by 1% formaldehyde at room temperature for 30 min. Following quenching the unused formaldehyde with 125 mM glycine at room temperature for 5 min, the cross-linked cells were harvested by centrifugation and washed 3 times with 50 mL of ice-cold TBS. The washed cells were resuspended in 0.5 ml of lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, protease inhibitor mixture (Sigma) and 1 kU Ready-Lyse lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 ml of 2  IP buffer composed of 100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 1 mM EDTA, 2% (vol/vol) Triton X-100, and protease inhibitor mixture (Sigma). The lysate was then sonicated 4 times for 20 sec each in an ice bath to fragment the chromatin complexes. Cell debris was removed by centrifugation at 13,000 rpm at 4  C for 10 min. To immunoprecipitate the protein-DNA complexes, the antibody was then added into the cell extract. For the control (mock-IP), 2 ug of normal mouse IgG (Upstate) was added into the cell extract. They were then incubated overnight at 4  C, and 50   l of the Dynabeads Pan mouse IgG magnetic beads (Invitrogen) was added into the mixture. After 5-h incubation at 4  C, the beads were washed twice with the IP buffer [50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1 mM EDTA, 1% (vol/vol) Triton X-100, and protease inhibitor mixture], once with the wash buffer I [50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% (vol/vol) Triton X-100, and 1 mM EDTA], once with wash buffer II [10 mM Tris-HCl buffer (pH 8.0), 250 mM LiCl, 1% (vol/vol) Triton X-100, and 1 mM EDTA], and once with TE buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA] in order. After removing the TE buffer, the beads were resuspended in 200 ul of elution buffer [50 mM Tris-HCl (pH 8.0), 10 mM EDTA and 1% SDS] and incubated overnight at 65  C for reverse cross-linking. After reversal of the cross-links, RNAs were removed by incubation with 200uL of TE buffer with 1uL of RNaseA (Qiagen) for 2 h at 37  C. Proteins in the DNA sample were then removed by incubation with 4uL of proteinase K solution (Invitrogen) for 2 h at 55  C. The sample was then purified with a PCR purification kit (Qiagen).

tag: phenotype

value: pathogenic, capsular

tag: antibody

value: anti-sigmaD

tag: vendor/catalog

value: neoclone #W0004

source_name: Mock IP DNA

value: normal mouse IgG


title: Pol II_100min_rep2

city: Cambridge

address: Downing Street

department: PDN

country: United Kingdom

hyb_protocol: 34 µg labeled sample DNA and 34 µg labeled control DNA were combined, dried in a speed vac with medium heat and resuspended in 12.3 µl water.  For each hybridisation, 29.5µl 2X Hybridization Buffer, 11.8µl Hybridization Component A and 1.2µl Alignment Oligo (NimbleGen Hybridization Kit) were combined and 31.7µl added to each hybridisation sample. Samples were incubated at +95°C for 5 minutes, 42°C for 5 minutes and 41 µl loaded onto the array. The hybridisation was performed to NimbleGen D. melanogaster ChIP-chip 2.1M Whole-Genome Tiling Arrays in the Nimbelegen hybridisation station at 42°C (mix mode B) for 18 hours. Post-hybridisation washes were performed according to the NimbleGen Wash Buffer Kit instructions.

organism: Drosophila melanogaster

label_protocol: In duplicate reactions: 1 μg of amplified DNA with 30 µl 2.5X Random Primers Solution (BioPrime DNA labelling kit, Life Technologies) was incubated at 100°C for 5 minutes and then cooled on ice. The samples were labelled as technical dye-swap replicates using the BioPrime DNA labelling kit (Life Technologies) in the presence of 4.5nmol fluorescently labelled Cy3- or Cy5-dCTP (GE Healthcare) and 72 U of Klenow at 37°C. After 2 hours the reactions were stopped with 7.5 µl Stop Buffer (BioPrime DNA labelling kit, Life Technologies). Duplicate reactions were pooled into single tubes and then precipitated with 165 µl Isopropanol and 0.2M sodium chloride and washed with cold 80% ethanol. The DNA was resuspened in 50 µl water and quantified on a Nanodrop spectrophotometer (Thermo Scientific).

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 100 minutes.

tag: treatment

tag: time point

tag: chip antibody

tag: antibody vendor


title: Pol II_100min_rep3


title: primary granulosa cells, biological repeat 1

city: Taipei

first: Chun

middle: Ying

last: Yu

address: 128 Academia Road, Section 2

department: Genomic Research center

country: Taiwan

institute: Academia sinica

description:
Gra1
Gene expression data from granulosa cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned with an Affymetrix GeneChip Scanner 7G.

data_processing: Global scaling was used as the normalization method.

organism: Homo sapiens

source_name: granulosa cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Pluripotent cells were grown on MEF feeders in DMEM/F12 medium plus 20% Knockout Serum Replacement and bFGF. The parental cells were grown in DMDM plus 10% FBS.

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

treatment_protocol: None.

tag: cell type

value: primary granulosa cells

tag: gender

value: female


title: HeDiPig_F5


title: primary dermal papilla cells, biological repeat 2

description:
DPC2
Gene expression data from DPC.

source_name: adult male dermal papilla cells

value: primary dermal papilla cells

value: male

value: adult


title: HeDiPig_F4

source_name: milk line from fetus taken at 63 day post conception

value: 63 dpc


title: Pol II_60min_rep3

source_name: Pol II ChIP DNA after 60 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 60 minutes.

value: Notch stimulation

value: 60 min

source_name: Total input after 60 min. Notch activation


title: iDPC subclone 3, biological repeat 1

description:
iDPC3-1
Gene expression data from iDPC.

source_name: induced pluripotency cells from DPC, subclone 3

value: induced pluripotency cells from DPC

tag: subclone


title: RNA polymerase binding site identification experiment 3

description: ChIP-chip for RNA polymerase binding site identification in Klebsiella pneumoniae MGH 78578

source_name: RNA polymerase ChIP DNA

value: anti-sigmaBeta

value: neoclone #WP002


title: Pol II_60min_rep1

value: Pol II (Ser 2 and Ser 5 phosphorylated) antibody

value: Abcam


title: RNA polymerase binding site identification experiment 2

value: pathogenic, capsular


title: KP_statphase_exp3

description: This sample is of wild-type Klebsiella pneumoniad MGH 78578. It is the third of three wild-type technical replicates used in this experiment, each from same culture harvested in stationary phase (OD ~ 1.3)

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: wild type cells

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Glucose M9 minimal media was used as a culture media. Glucose (2 g/L) M9 minimal media is composed of 2 ml/L of 1 M MgSO4, 50 μl/L of 1 M CaCl2, 12.8 g/L Na2HPO4•7H2O, 3 g/L KH2PO4, 0.5 g/L NaCl, 1 g/L NH4Cl and 1 ml trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4•7H2O, 198 mg MnCl2•4H2O, 254 mg CoCl2•6H2O, 13.4 mg CuCl2, and 147 mg CaCl2. Three milliliters of cell culture media in mid-log (OD=0.6) phase or

extract_protocol: Cultures were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen). Samples were immediately vortexed for 5 seconds, and further incubated for 5 minutes at room temperature. After that, samples were centrifuged at 5000 g for 10 minutes. The supernatant was removed with no residual supernatant. Total RNA samples were then isolated using RNeasy Plus Mini kit (Qiagen) by following the manufacturer’s manual.

tag: genotype/variation

value: wild type

tag: Stage

value: stationary growth phase

value: Capsular

tag: accession


title: igra subclone 2, biological repeat 1

description:
iGra2-1
Gene expression data from iGra cells.

source_name: induced pluripotency cells from granulosa cells, subclone 2


title: Pol II_30min_rep2

source_name: Total input after 30 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 30 minutes.

tag: cell line

value: 30 min

source_name: Pol II ChIP DNA after 30 min. Notch activation

tag: antibody catalog #


title: Pol II_40min_rep3

source_name: Pol II ChIP DNA after 40 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 40 minutes.

value: 40 min

source_name: Total input after 40 min. Notch activation


title: Pol II_40min_rep2


title: KP_statphase_exp2

description: This sample is of wild-type Klebsiella pneumoniad MGH 78578. It is the second of three wild-type technical replicates used in this experiment, each from same culture harvested in stationary phase (OD ~ 1.3)


title: Pol II_40min_rep1


title: Pol II_30min_rep3


title: KP_statphase_exp1

description: This sample is of wild-type Klebsiella pneumoniad MGH 78578. It is the first of three wild-type technical replicates used in this experiment, each from same culture harvested in stationary phase (OD ~ 1.3)


title: HeDiPig_F1

tag: tissue

value: nipple

tag: breed

value: German landrace


title: inactive HUMSC

first: Kuo-Ching

last: Chao

address: 252, Wu Hsing Street

department: Department of Internal Medicine

institute: Taipei Medical University Hospital

description:
Gene expression data from inactive HUMSC
HST

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

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

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

source_name: human umbilical cord

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

growth_protocol: HST and UC were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: UCHY was UC cells but cultured in 2% O2 incubator at 37℃ for 3 days

value: umbilical cord

value: mesenchymal stem cell (HUMSC)

tag: tumor suppression

value: low


title: primary dermal papilla cells, biological repeat 1

description:
DPC1
Gene expression data from DPC.

value: primary dermal papilla cells

value: male

tag: developmental stage

value: adult


title: HeDiPig_F3

value: 63 dpc


title: Curcumin_4 / Control_4 biol. Rep. 4; tech. Rep. 2

status: Public on Dec 30 2012

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

hyb_protocol: Samples were combined and hybridized to a custom oligoarray with 4 x 44k elements manufactured by Agilent Technologies (GPL8606). Hybridization and washing steps were performed according to Agilent instructions.

scan_protocol: The washed slides were scanned using GenePix4000B (Molecular Devices) scanner.

data_processing: Data was extracted using Feature Extraction software (Agilent Technologies), the background subtracted intensities (gProcessedSignal and rProcessedSignal) were LOWESS normalized.  Log2 ratio (Treated/Control) intensities was calculated.

organism: Schistosoma mansoni

label_protocol: All samples were linearly amplified and labeled using Agilent protocol with Low input RNA amplification kit

growth_protocol: Adult worms were obtained by portal perfusion of 56-days infected hamsters

extract_protocol: RNA from all samples was extract using Trizol reagent (Invitrogen) followed by DNase treatment using RNeasy kit (QIAGEN) according to manufacturer´s instructions.

treatment_protocol: Adult worms were kept in culture for 24 h with Curcumin (15uM) or the vehicle solution (DMSO)

value: Adult worms

value: culture with DMSO (Non-treated) for 24 h

value: culture with Curcumin (15 μM ) for 24 h


title: active HUMSC

description:
Gene expression data from active HUMSC
UC

value: high


title: Pol II_30min_rep1

value: Notch stimulation

value: Pol II (Ser 2 and Ser 5 phosphorylated) antibody

value: Abcam


title: Curcumin_3 / Control_3 biol. Rep. 3; tech. Rep. 2


title: active HUMSC culture in hypoxia condition

description:
Gene expression data from active HUMSC
UCHY

tag: growth condition

value: hypoxia


title: Pol II_20min_rep3

source_name: Pol II ChIP DNA after 20 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 20 minutes.

tag: treatment

value: 20 min

source_name: Total input after 20 min. Notch activation


title: HeDiPig_F2

value: nipple

value: German landrace


title: Curcumin_4 / Control_4 biol. Rep. 4; tech. Rep. 1


title: Pol II_20min_rep1

tag: time point


title: KP_logphase_exp3

description: This sample is of wild-type Klebsiella pneumoniad MGH 78578. It is the third of three wild-type technical replicates used in this experiment, each from same culture harvested in mid-log phase (OD ~ 0.6)

value: wild type

value: exponential growth phase

tag: phenotype

value: Capsular


title: Curcumin_2 / Control_2 biol. Rep. 2; tech. Rep. 1


title: Curcumin_1 / Control_1 biol. Rep. 1; tech. Rep. 1


title: Curcumin_1 / Control_1 biol. Rep. 1; tech. Rep. 2


title: Curcumin_2 / Control_2 biol. Rep. 2; tech. Rep. 2


title: RNA polymerase binding site identification experiment 1

value: pathogenic, capsular

tag: antibody

value: anti-sigmaBeta

tag: vendor/catalog

value: neoclone #WP002

source_name: Mock IP DNA

value: normal mouse IgG


title: iDPC subclone 3, biological repeat 2

description:
iDPC3-2
Gene expression data from iDPC.

tag: cell type

value: induced pluripotency cells from DPC

tag: gender

value: male


title: Perigonadal adipose tissue at day 14, biological replication ID J51

city: Seattle

first: Zhi

last: Wang

state: WA

address: 1100 Fairview Ave N, M1-C108

institute: Sage Bionetworks

hyb_protocol: RNA was hybridized to Affymetrix array according to the manufacturer instructions.

scan_protocol: GeneChip mouse genome 430 2.0 microarrays were scanned according to the manufacturer instructions.

data_processing: Raw data were background subtracted and quantile normalized using Rosetta Resolver software

organism: Mus musculus

source_name: Mouse Perigonadal adipose tissue after 14 days of caloric restriction

label_protocol: RNA was labeled according to the manufacturer instructions.

extract_protocol: Total RNA was extracted according to the manufacturer instructions.

tag: strain

value: Male

value: Perigonadal adipose


title: Curcumin_3 / Control_3 biol. Rep. 3; tech. Rep. 1

value: Adult worms

value: culture with Curcumin (15 μM ) for 24 h

value: culture with DMSO (Non-treated) for 24 h


title: Perigonadal adipose tissue at day 42, biological replication ID N69

source_name: Mouse Perigonadal adipose tissue after 42 days of caloric restriction


title: HeDiPig_F7

source_name: milk line from fetus taken at 91 day post conception

value: 91 dpc


title: Perigonadal adipose tissue at day 0, biological replication ID N50

source_name: Mouse Perigonadal adipose tissue after 0 days of caloric restriction


title: Perigonadal adipose tissue at day 60, biological replication ID N82

source_name: Mouse Perigonadal adipose tissue after 60 days of caloric restriction


title: Perigonadal adipose tissue at day 7, biological replication ID N44

source_name: Mouse Perigonadal adipose tissue after 7 days of caloric restriction


title: Perigonadal adipose tissue at day 0, biological replication ID J17


title: Pol II_10min_rep3

source_name: Pol II ChIP DNA after 10 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 10 minutes.

value: Notch stimulation

value: 10 min

tag: chip antibody

value: Pol II (Ser 2 and Ser 5 phosphorylated) antibody

tag: antibody vendor

value: Abcam

source_name: Total input after 10 min. Notch activation


title: Perigonadal adipose tissue at day 0, biological replication ID N72


title: Pol II_10min_rep2

tag: cell line


title: Pol II_60min_rep2

source_name: Total input after 60 min. Notch activation

value: 60 min

source_name: Pol II ChIP DNA after 60 min. Notch activation

tag: antibody catalog #


title: Perigonadal adipose tissue at day 3, biological replication ID N12

source_name: Mouse Perigonadal adipose tissue after 3 days of caloric restriction

tag: tissue


title: Perigonadal adipose tissue at day 14, biological replication ID J47


title: Perigonadal adipose tissue at day 0, biological replication ID N74


title: Perigonadal adipose tissue at day 42, biological replication ID J55


title: KP_logphase_exp2

description: This sample is of wild-type Klebsiella pneumoniad MGH 78578. It is the second of three wild-type technical replicates used in this experiment, each from same culture harvested in mid-log phase (OD ~ 0.6)

source_name: wild type cells

tag: genotype/variation

value: wild type

tag: Stage

value: exponential growth phase

value: Capsular

tag: accession


title: Perigonadal adipose tissue at day 14, biological replication ID N98


title: Perigonadal adipose tissue at day 21, biological replication ID N91

source_name: Mouse Perigonadal adipose tissue after 21 days of caloric restriction


title: Perigonadal adipose tissue at day 14, biological replication ID N35


title: Pol II_20min_rep2

value: 20 min


title: Perigonadal adipose tissue at day 7, biological replication ID J34


title: Perigonadal adipose tissue at day 7, biological replication ID N97


title: KP_logphase_exp1

description: This sample is of wild-type Klebsiella pneumoniad MGH 78578. It is the first of three wild-type technical replicates used in this experiment, each from same culture harvested in mid-log phase (OD ~ 0.6)


title: Pol II_10min_rep1


title: Pol II_0min_rep2

source_name: Total input after 0 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 0 minutes.

value: 0 min

source_name: Pol II ChIP DNA after 0 min. Notch activation


title: Perigonadal adipose tissue at day 42, biological replication ID J21


title: Perigonadal adipose tissue at day 42, biological replication ID J30


title: Perigonadal adipose tissue at day 14, biological replication ID N33


title: Perigonadal adipose tissue at day 7, biological replication ID N39


title: Perigonadal adipose tissue at day 60, biological replication ID N22


title: Perigonadal adipose tissue at day 42, biological replication ID N20


title: Pol II_0min_rep1


title: Perigonadal adipose tissue at day 14, biological replication ID J14


title: Perigonadal adipose tissue at day 42, biological replication ID N10


title: Perigonadal adipose tissue at day 3, biological replication ID J11


title: Perigonadal adipose tissue at day 60, biological replication ID N14


title: Perigonadal adipose tissue at day 42, biological replication ID N92


title: Perigonadal adipose tissue at day 3, biological replication ID N7


title: Perigonadal adipose tissue at day 7, biological replication ID J6


title: Perigonadal adipose tissue at day 42, biological replication ID N37


title: Perigonadal adipose tissue at day 0, biological replication ID J5


title: Pol II_0min_rep3


title: Perigonadal adipose tissue at day 3, biological replication ID N13


title: Perigonadal adipose tissue at day 21, biological replication ID N3


title: Perigonadal adipose tissue at day 21, biological replication ID J91


title: Perigonadal adipose tissue at day 7, biological replication ID J44


title: Perigonadal adipose tissue at day 3, biological replication ID J23


title: Perigonadal adipose tissue at day 3, biological replication ID N2


title: Perigonadal adipose tissue at day 1, biological replication ID J60

source_name: Mouse Perigonadal adipose tissue after 1 days of caloric restriction


title: Perigonadal adipose tissue at day 1, biological replication ID J80


title: Perigonadal adipose tissue at day 14, biological replication ID J13


title: Perigonadal adipose tissue at day 21, biological replication ID N99


title: Perigonadal adipose tissue at day 21, biological replication ID J10


title: Perigonadal adipose tissue at day 3, biological replication ID J16


title: Perigonadal adipose tissue at day 60, biological replication ID N43


title: Perigonadal adipose tissue at day 21, biological replication ID J2


title: Perigonadal adipose tissue at day 3, biological replication ID 32


title: Perigonadal adipose tissue at day 60, biological replication ID N62


title: Perigonadal adipose tissue at day 0, biological replication ID N45


title: Perigonadal adipose tissue at day 7, biological replication ID J22


title: Perigonadal adipose tissue at day 1, biological replication ID J20


title: Perigonadal adipose tissue at day 14, biological replication ID J57


title: Perigonadal adipose tissue at day 14, biological replication ID N93


title: Perigonadal adipose tissue at day 42, biological replication ID J36


title: Perigonadal adipose tissue at day 7, biological replication ID N15


title: Perigonadal adipose tissue at day 60, biological replication ID N59


title: Perigonadal adipose tissue at day 1, biological replication ID J15


title: Perigonadal adipose tissue at day 0, biological replication ID J40


title: Perigonadal adipose tissue at day 21, biological replication ID J1


title: Perigonadal adipose tissue at day 0, biological replication ID N30


title: Perigonadal adipose tissue at day 0, biological replication ID J53


title: Perigonadal adipose tissue at day 21, biological replication ID N80


title: Perigonadal adipose tissue at day 1, biological replication ID J7


title: Perigonadal adipose tissue at day 3, biological replication ID N90


title: Perigonadal adipose tissue at day 7, biological replication ID N16


title: Perigonadal adipose tissue at day 7, biological replication ID J25


title: Perigonadal adipose tissue at day 3, biological replication ID J12


title: Perigonadal adipose tissue at day 0, biological replication ID J42


title: Perigonadal adipose tissue at day 0, biological replication ID J43


title: Perigonadal adipose tissue at day 14, biological replication ID J26


title: Perigonadal adipose tissue at day 7, biological replication ID N0


title: Perirenal adipose tissue at day 3, biological replication ID J12

source_name: Mouse Perirenal adipose tissue after 3 days of caloric restriction

value: Perirenal adipose


title: Perirenal adipose tissue at day 7, biological replication ID J22

source_name: Mouse Perirenal adipose tissue after 7 days of caloric restriction

value: Male


title: Perirenal adipose tissue at day 7, biological replication ID N44


title: Perirenal adipose tissue at day 3, biological replication ID N13


title: Perirenal adipose tissue at day 0, biological replication ID N74

source_name: Mouse Perirenal adipose tissue after 0 days of caloric restriction


title: Perigonadal adipose tissue at day 21, biological replication ID N11

value: Perigonadal adipose


title: Perigonadal adipose tissue at day 21, biological replication ID J8


title: Perirenal adipose tissue at day 7, biological replication ID N39


title: Perigonadal adipose tissue at day 42, biological replication ID N70

source_name: Mouse Perigonadal adipose tissue after 42 days of caloric restriction


title: Perigonadal adipose tissue at day 21, biological replication ID J3


title: Perirenal adipose tissue at day 14, biological replication ID N98

source_name: Mouse Perirenal adipose tissue after 14 days of caloric restriction


title: Perirenal adipose tissue at day 42, biological replication ID J4

source_name: Mouse Perirenal adipose tissue after 42 days of caloric restriction


title: Perirenal adipose tissue at day 7, biological replication ID N97


title: Perirenal adipose tissue at day 42, biological replication ID N69


title: Perirenal adipose tissue at day 21, biological replication ID J8

source_name: Mouse Perirenal adipose tissue after 21 days of caloric restriction


title: Perirenal adipose tissue at day 3, biological replication ID N7


title: Perirenal adipose tissue at day 1, biological replication ID J60

source_name: Mouse Perirenal adipose tissue after 1 days of caloric restriction


title: Perigonadal adipose tissue at day 3, biological replication ID J9


title: Perirenal adipose tissue at day 14, biological replication ID J57


title: Perirenal adipose tissue at day 21, biological replication ID N11


title: Perirenal adipose tissue at day 60, biological replication ID N62

source_name: Mouse Perirenal adipose tissue after 60 days of caloric restriction


title: Perirenal adipose tissue at day 60, biological replication ID N22


title: Perirenal adipose tissue at day 0, biological replication ID J42


title: Perirenal adipose tissue at day 3, biological replication ID N2


title: Perirenal adipose tissue at day 14, biological replication ID J47


title: Perirenal adipose tissue at day 60, biological replication ID N82


title: Perirenal adipose tissue at day 14, biological replication ID N35


title: Perirenal adipose tissue at day 21, biological replication ID N80


title: Perirenal adipose tissue at day 0, biological replication ID J53


title: Perirenal adipose tissue at day 7, biological replication ID J52


title: Perirenal adipose tissue at day 7, biological replication ID J6


title: Perirenal adipose tissue at day 21, biological replication ID N26


title: Perirenal adipose tissue at day 3, biological replication ID J9


title: Perirenal adipose tissue at day 42, biological replication ID N70


title: Perirenal adipose tissue at day 7, biological replication ID J25


title: Perirenal adipose tissue at day 1, biological replication ID J80


title: Perirenal adipose tissue at day 21, biological replication ID J3


title: Perirenal adipose tissue at day 42, biological replication ID J30


title: Perirenal adipose tissue at day 3, biological replication ID J23


title: Perirenal adipose tissue at day 3, biological replication ID N90


title: Perirenal adipose tissue at day 0, biological replication ID N50


title: Perirenal adipose tissue at day 42, biological replication ID J36


title: Perirenal adipose tissue at day 42, biological replication ID J33


title: Perirenal adipose tissue at day 60, biological replication ID N14


title: Perirenal adipose tissue at day 21, biological replication ID N99


title: Perirenal adipose tissue at day 42, biological replication ID N20


title: Perirenal adipose tissue at day 42, biological replication ID J55


title: Perirenal adipose tissue at day 3, biological replication ID J16


title: Perirenal adipose tissue at day 1, biological replication ID J20


title: Perirenal adipose tissue at day 14, biological replication ID J51


title: Perirenal adipose tissue at day 1, biological replication ID J7


title: Perirenal adipose tissue at day 21, biological replication ID J2


title: Perirenal adipose tissue at day 0, biological replication ID J43


title: Perirenal adipose tissue at day 14, biological replication ID N33


title: Perirenal adipose tissue at day 0, biological replication ID J40


title: Perirenal adipose tissue at day 21, biological replication ID J91


title: Perirenal adipose tissue at day 42, biological replication ID N92


title: Perirenal adipose tissue at day 7, biological replication ID J34


title: Perirenal adipose tissue at day 0, biological replication ID N6


title: Perirenal adipose tissue at day 21, biological replication ID N91


title: Perirenal adipose tissue at day 21, biological replication ID J10


title: Perirenal adipose tissue at day 21, biological replication ID N3


title: Perirenal adipose tissue at day 14, biological replication ID J13


title: Perirenal adipose tissue at day 14, biological replication ID N93


title: Perirenal adipose tissue at day 7, biological replication ID J44


title: Perirenal adipose tissue at day 14, biological replication ID J14


title: Perirenal adipose tissue at day 60, biological replication ID N59


title: Perirenal adipose tissue at day 3, biological replication ID 32


title: Perirenal adipose tissue at day 7, biological replication ID N15


title: Perirenal adipose tissue at day 42, biological replication ID N37


title: Perirenal adipose tissue at day 21, biological replication ID J1


title: Perirenal adipose tissue at day 0, biological replication ID N30


title: Perirenal adipose tissue at day 7, biological replication ID N0


title: Perirenal adipose tissue at day 0, biological replication ID J5


title: Perirenal adipose tissue at day 1, biological replication ID J15


title: Perirenal adipose tissue at day 3, biological replication ID J11


title: Perirenal adipose tissue at day 0, biological replication ID N45


title: Perirenal adipose tissue at day 14, biological replication ID J26


title: Perirenal adipose tissue at day 3, biological replication ID N12


title: Perirenal adipose tissue at day 60, biological replication ID N43


title: Mesenteric adipose tissue at day 0, biological replication ID J17

source_name: Mouse Mesenteric adipose tissue after 0 days of caloric restriction

value: Mesenteric adipose


title: Perirenal adipose tissue at day 0, biological replication ID J17


title: Perirenal adipose tissue at day 42, biological replication ID N10


title: Perirenal adipose tissue at day 0, biological replication ID N72


title: Mesenteric adipose tissue at day 3, biological replication ID J11

source_name: Mouse Mesenteric adipose tissue after 3 days of caloric restriction


title: Mesenteric adipose tissue at day 21, biological replication ID N91

source_name: Mouse Mesenteric adipose tissue after 21 days of caloric restriction


title: Mesenteric adipose tissue at day 7, biological replication ID J44

source_name: Mouse Mesenteric adipose tissue after 7 days of caloric restriction


title: Mesenteric adipose tissue at day 14, biological replication ID N98

source_name: Mouse Mesenteric adipose tissue after 14 days of caloric restriction


title: Mesenteric adipose tissue at day 1, biological replication ID J15

source_name: Mouse Mesenteric adipose tissue after 1 days of caloric restriction


title: Mesenteric adipose tissue at day 60, biological replication ID N14

source_name: Mouse Mesenteric adipose tissue after 60 days of caloric restriction


title: Perirenal adipose tissue at day 7, biological replication ID N16


title: Perirenal adipose tissue at day 42, biological replication ID J21


title: Mesenteric adipose tissue at day 1, biological replication ID J20


title: Mesenteric adipose tissue at day 42, biological replication ID J33

source_name: Mouse Mesenteric adipose tissue after 42 days of caloric restriction


title: Mesenteric adipose tissue at day 3, biological replication ID J12


title: Mesenteric adipose tissue at day 42, biological replication ID N20


title: Mesenteric adipose tissue at day 3, biological replication ID N12


title: Mesenteric adipose tissue at day 42, biological replication ID N92


title: Mesenteric adipose tissue at day 14, biological replication ID J26


title: Mesenteric adipose tissue at day 21, biological replication ID N26


title: Mesenteric adipose tissue at day 42, biological replication ID N10


title: Mesenteric adipose tissue at day 7, biological replication ID J22


title: Mesenteric adipose tissue at day 7, biological replication ID J25


title: Mesenteric adipose tissue at day 1, biological replication ID J80


title: Mesenteric adipose tissue at day 42, biological replication ID J55


title: Mesenteric adipose tissue at day 21, biological replication ID J3


title: Mesenteric adipose tissue at day 21, biological replication ID J2


title: Mesenteric adipose tissue at day 42, biological replication ID N70


title: Mesenteric adipose tissue at day 3, biological replication ID N13


title: Mesenteric adipose tissue at day 14, biological replication ID J13


title: Mesenteric adipose tissue at day 21, biological replication ID N11


title: Mesenteric adipose tissue at day 21, biological replication ID J10


title: Mesenteric adipose tissue at day 7, biological replication ID N97


title: Mesenteric adipose tissue at day 1, biological replication ID J7


title: Mesenteric adipose tissue at day 60, biological replication ID N43


title: Mesenteric adipose tissue at day 0, biological replication ID N74


title: Mesenteric adipose tissue at day 21, biological replication ID N3


title: Mesenteric adipose tissue at day 3, biological replication ID J9


title: Mesenteric adipose tissue at day 0, biological replication ID N30


title: Mesenteric adipose tissue at day 0, biological replication ID N6


title: Mesenteric adipose tissue at day 42, biological replication ID N69


title: Mesenteric adipose tissue at day 7, biological replication ID N15


title: Mesenteric adipose tissue at day 3, biological replication ID J23


title: Mesenteric adipose tissue at day 14, biological replication ID N33


title: Mesenteric adipose tissue at day 42, biological replication ID J21


title: Mesenteric adipose tissue at day 14, biological replication ID J47


title: Mesenteric adipose tissue at day 7, biological replication ID N39


title: Mesenteric adipose tissue at day 7, biological replication ID N16


title: Mesenteric adipose tissue at day 60, biological replication ID N59


title: Mesenteric adipose tissue at day 60, biological replication ID N22


title: Mesenteric adipose tissue at day 0, biological replication ID J5


title: Mesenteric adipose tissue at day 7, biological replication ID N44


title: Mesenteric adipose tissue at day 3, biological replication ID N2


title: Mesenteric adipose tissue at day 0, biological replication ID J53


title: Mesenteric adipose tissue at day 3, biological replication ID J16


title: Mesenteric adipose tissue at day 21, biological replication ID N99


title: Mesenteric adipose tissue at day 7, biological replication ID J6


title: Mesenteric adipose tissue at day 0, biological replication ID J43


title: Mesenteric adipose tissue at day 60, biological replication ID N62


title: Mesenteric adipose tissue at day 21, biological replication ID J91


title: Mesenteric adipose tissue at day 21, biological replication ID J8


title: Mesenteric adipose tissue at day 3, biological replication ID 32


title: Mesenteric adipose tissue at day 7, biological replication ID N0


title: Mesenteric adipose tissue at day 14, biological replication ID J51


title: Mesenteric adipose tissue at day 14, biological replication ID N93


title: Mesenteric adipose tissue at day 14, biological replication ID J14


title: Mesenteric adipose tissue at day 21, biological replication ID J1


title: Mesenteric adipose tissue at day 0, biological replication ID J40


title: Mesenteric adipose tissue at day 1, biological replication ID J60


title: Mesenteric adipose tissue at day 14, biological replication ID J57


title: Mesenteric adipose tissue at day 60, biological replication ID N82


title: Mesenteric adipose tissue at day 42, biological replication ID J36


title: Mesenteric adipose tissue at day 42, biological replication ID N37


title: Mesenteric adipose tissue at day 3, biological replication ID N7


title: Mesenteric adipose tissue at day 21, biological replication ID N80


title: Mesenteric adipose tissue at day 0, biological replication ID J42


title: Mesenteric adipose tissue at day 7, biological replication ID J52


title: Subcutaneous adipose tissue at day 1, biological replication ID J15

source_name: Mouse Subcutaneous adipose tissue after 1 days of caloric restriction

value: Subcutaneous adipose


title: Subcutaneous adipose tissue at day 14, biological replication ID J13

source_name: Mouse Subcutaneous adipose tissue after 14 days of caloric restriction


title: Mesenteric adipose tissue at day 0, biological replication ID N72


title: Subcutaneous adipose tissue at day 21, biological replication ID J3

source_name: Mouse Subcutaneous adipose tissue after 21 days of caloric restriction


title: Mesenteric adipose tissue at day 7, biological replication ID J34


title: Subcutaneous adipose tissue at day 14, biological replication ID J14


title: Subcutaneous adipose tissue at day 21, biological replication ID J2


title: Subcutaneous adipose tissue at day 21, biological replication ID J8


title: Subcutaneous adipose tissue at day 3, biological replication ID J16

source_name: Mouse Subcutaneous adipose tissue after 3 days of caloric restriction


title: Subcutaneous adipose tissue at day 7, biological replication ID J6

source_name: Mouse Subcutaneous adipose tissue after 7 days of caloric restriction


title: Subcutaneous adipose tissue at day 1, biological replication ID J7


title: Subcutaneous adipose tissue at day 3, biological replication ID J12


title: Subcutaneous adipose tissue at day 21, biological replication ID J10


title: Subcutaneous adipose tissue at day 21, biological replication ID J1


title: Mesenteric adipose tissue at day 3, biological replication ID N90


title: Mesenteric adipose tissue at day 42, biological replication ID J30


title: Mesenteric adipose tissue at day 14, biological replication ID N35


title: Subcutaneous adipose tissue at day 42, biological replication ID J4

source_name: Mouse Subcutaneous adipose tissue after 42 days of caloric restriction


title: Subcutaneous adipose tissue at day 3, biological replication ID J11


title: Subcutaneous adipose tissue at day 3, biological replication ID N12


title: Mesenteric adipose tissue at day 0, biological replication ID N45


title: Subcutaneous adipose tissue at day 42, biological replication ID N92


title: Subcutaneous adipose tissue at day 21, biological replication ID N11


title: Subcutaneous adipose tissue at day 3, biological replication ID J9


title: Subcutaneous adipose tissue at day 7, biological replication ID N15


title: Subcutaneous adipose tissue at day 42, biological replication ID N70


title: Subcutaneous adipose tissue at day 0, biological replication ID J5

source_name: Mouse Subcutaneous adipose tissue after 0 days of caloric restriction


title: Subcutaneous adipose tissue at day 0, biological replication ID J17


title: Subcutaneous adipose tissue at day 3, biological replication ID J23


title: Subcutaneous adipose tissue at day 60, biological replication ID N22

source_name: Mouse Subcutaneous adipose tissue after 60 days of caloric restriction


title: Subcutaneous adipose tissue at day 0, biological replication ID J40


title: Subcutaneous adipose tissue at day 42, biological replication ID J21


title: Subcutaneous adipose tissue at day 7, biological replication ID N39


title: Subcutaneous adipose tissue at day 60, biological replication ID N82


title: Subcutaneous adipose tissue at day 21, biological replication ID N3


title: Subcutaneous adipose tissue at day 14, biological replication ID J47


title: Subcutaneous adipose tissue at day 0, biological replication ID J53


title: Subcutaneous adipose tissue at day 7, biological replication ID J22


title: Subcutaneous adipose tissue at day 0, biological replication ID N30


title: Subcutaneous adipose tissue at day 21, biological replication ID N91


title: Subcutaneous adipose tissue at day 7, biological replication ID J52


title: Subcutaneous adipose tissue at day 3, biological replication ID N7


title: Subcutaneous adipose tissue at day 42, biological replication ID N10


title: Subcutaneous adipose tissue at day 0, biological replication ID J43


title: Subcutaneous adipose tissue at day 42, biological replication ID J36


title: Mesenteric adipose tissue at day 0, biological replication ID N50


title: Subcutaneous adipose tissue at day 60, biological replication ID N59


title: Subcutaneous adipose tissue at day 42, biological replication ID J55


title: Subcutaneous adipose tissue at day 14, biological replication ID N93


title: Subcutaneous adipose tissue at day 42, biological replication ID J33


title: Subcutaneous adipose tissue at day 1, biological replication ID J20


title: Subcutaneous adipose tissue at day 3, biological replication ID N90


title: Subcutaneous adipose tissue at day 7, biological replication ID J25


title: Subcutaneous adipose tissue at day 1, biological replication ID J80


title: Subcutaneous adipose tissue at day 60, biological replication ID N62


title: Subcutaneous adipose tissue at day 60, biological replication ID N14


title: Subcutaneous adipose tissue at day 3, biological replication ID N13


title: Subcutaneous adipose tissue at day 1, biological replication ID J60


title: Subcutaneous adipose tissue at day 0, biological replication ID N74


title: Subcutaneous adipose tissue at day 21, biological replication ID N80


title: Subcutaneous adipose tissue at day 21, biological replication ID N26


title: Subcutaneous adipose tissue at day 0, biological replication ID N50


title: Subcutaneous adipose tissue at day 7, biological replication ID J34


title: Subcutaneous adipose tissue at day 7, biological replication ID J44


title: Subcutaneous adipose tissue at day 7, biological replication ID N44


title: Subcutaneous adipose tissue at day 7, biological replication ID N97


title: Subcutaneous adipose tissue at day 0, biological replication ID J42


title: Subcutaneous adipose tissue at day 7, biological replication ID N16


title: Subcutaneous adipose tissue at day 0, biological replication ID N6


title: Subcutaneous adipose tissue at day 42, biological replication ID N37


title: Subcutaneous adipose tissue at day 0, biological replication ID N45


title: Subcutaneous adipose tissue at day 0, biological replication ID N72


title: Subcutaneous adipose tissue at day 42, biological replication ID N69


title: Subcutaneous adipose tissue at day 14, biological replication ID J57


title: Subcutaneous adipose tissue at day 42, biological replication ID N20


title: Subcutaneous adipose tissue at day 14, biological replication ID N98


title: Subcutaneous adipose tissue at day 60, biological replication ID N43


title: Subcutaneous adipose tissue at day 3, biological replication ID 32


title: Liver tissue at day 3, biological replication ID N7

source_name: Mouse Liver tissue after 3 days of caloric restriction

value: Liver


title: Subcutaneous adipose tissue at day 21, biological replication ID N99


title: Liver tissue at day 3, biological replication ID J9


title: Liver tissue at day 14, biological replication ID N93

source_name: Mouse Liver tissue after 14 days of caloric restriction


title: Subcutaneous adipose tissue at day 14, biological replication ID J26


title: Subcutaneous adipose tissue at day 7, biological replication ID N0


title: Liver tissue at day 0, biological replication ID N45

source_name: Mouse Liver tissue after 0 days of caloric restriction


title: Liver tissue at day 3, biological replication ID N12


title: Liver tissue at day 21, biological replication ID J2

source_name: Mouse Liver tissue after 21 days of caloric restriction


title: Liver tissue at day 14, biological replication ID N33


title: Subcutaneous adipose tissue at day 14, biological replication ID J51


title: Liver tissue at day 60, biological replication ID N59

source_name: Mouse Liver tissue after 60 days of caloric restriction


title: Liver tissue at day 14, biological replication ID J26


title: Liver tissue at day 60, biological replication ID N22


title: Liver tissue at day 7, biological replication ID J34

source_name: Mouse Liver tissue after 7 days of caloric restriction


title: Liver tissue at day 42, biological replication ID N92

source_name: Mouse Liver tissue after 42 days of caloric restriction


title: Subcutaneous adipose tissue at day 21, biological replication ID J91


title: Subcutaneous adipose tissue at day 3, biological replication ID N2


title: Liver tissue at day 60, biological replication ID N82


title: Liver tissue at day 1, biological replication ID J15

source_name: Mouse Liver tissue after 1 days of caloric restriction


title: Liver tissue at day 7, biological replication ID J52


title: Subcutaneous adipose tissue at day 14, biological replication ID N35


title: Liver tissue at day 0, biological replication ID N74


title: Liver tissue at day 7, biological replication ID N16


title: Liver tissue at day 0, biological replication ID J17


title: Liver tissue at day 7, biological replication ID J25


title: Liver tissue at day 21, biological replication ID N11


title: Liver tissue at day 7, biological replication ID N39


title: Liver tissue at day 7, biological replication ID J6


title: Liver tissue at day 7, biological replication ID J22


title: Liver tissue at day 14, biological replication ID J57


title: Liver tissue at day 0, biological replication ID N72


title: Liver tissue at day 7, biological replication ID N15


title: Liver tissue at day 0, biological replication ID N50


title: Liver tissue at day 21, biological replication ID J1


title: Liver tissue at day 0, biological replication ID J42


title: Liver tissue at day 14, biological replication ID N35


title: Liver tissue at day 42, biological replication ID N70


title: Liver tissue at day 21, biological replication ID J8


title: Liver tissue at day 14, biological replication ID J13


title: Liver tissue at day 3, biological replication ID J12


title: trtA-24_3_1_0_bh

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: untreated

hyb_protocol: Illumina standard procedure

scan_protocol: Illumina standard procedure on Illumina BeadStation 500 (Illumina, San Diego, CA)

data_processing: Transcript average-intensity signals were calculated with BeadStudio without background correction. Raw data were analyzed using Bioconductor (R 2.12.0, Bioconductor 2.7, oneChannelGUI 1.16.5). Average transcript intensities were log2 transformed and normalized by loess method

source_name: PC-3 untreated 24 hours

label_protocol: Illumina® TotalPrep™ RNA Amplification Kits (Ambion)

growth_protocol: human prostate adenocarcinoma cell line PC-3 was obtained from the American Type Culture Collection (Manassas, VA). Cells were cultured as monolayers in flasks using RPMI-1640 supplemented with 10% FBS.

extract_protocol: RNeasy Midi kit (Qiagen, Hilden, Germany)

treatment_protocol: Cells (2x10^6) were seeded in T150 flasks and then treated with vehicle (ctrl), with 5.5 μM of inactive cyclophosphamide (trt) or active 4-Hydro peroxy cyclophosphamide (trtA) for 10, 24, and 48 hours.

tag: treatment group

value: untreated

tag: treatment time

value: 24 hours


title: trtA-48_6_0_1_bf

description: 4-Hydro peroxy cyclophosphamide

source_name: PC-3 active compound 48 hours

value: 4-Hydro peroxy cyclophosphamide

value: 48 hours


title: trtA-48_5_1_0_bl

description: untreated

source_name: PC-3 untreated 48 hours


title: trtA-10_1_1_0_bg

description: untreated

source_name: PC-3 untreated 10 hours

value: 10 hours


title: trtA-24_3_1_0_bc

description: untreated


title: trtA-10_2_0_1_bb

description: 4-Hydro peroxy cyclophosphamide

source_name: PC-3 active compound 10 hours


title: trtA-10_1_1_0_ba

description: untreated


title: Liver tissue at day 1, biological replication ID J60


title: Liver tissue at day 21, biological replication ID N3


title: trtA-24_4_0_1_bd

description: 4-Hydro peroxy cyclophosphamide

source_name: PC-3 active compound 24 hours


title: Liver tissue at day 42, biological replication ID J21


title: trt-48_6_0_1_ar

description: inactive cyclophosphamide

source_name: PC-3 inactive compound 48 hours

value: inactive cyclophosphamide


title: Liver tissue at day 42, biological replication ID N69


title: trtA-10_2_0_1_at

description: 4-Hydro peroxy cyclophosphamide


title: Liver tissue at day 60, biological replication ID N62


title: Liver tissue at day 3, biological replication ID J23


title: trtA-24_3_1_0_au

description: untreated


title: Liver tissue at day 1, biological replication ID J20


title: trtA-48_6_0_1_bm

description: 4-Hydro peroxy cyclophosphamide


title: trtA-24_4_0_1_bi

description: 4-Hydro peroxy cyclophosphamide


title: trtA-48_5_1_0_be

description: untreated


title: Liver tissue at day 0, biological replication ID N30


title: Liver tissue at day 7, biological replication ID N44


title: trtA-10_1_1_0_as

description: untreated


title: trtA-48_6_0_1_az

description: 4-Hydro peroxy cyclophosphamide


title: Liver tissue at day 21, biological replication ID J10


title: Liver tissue at day 0, biological replication ID J53


title: trt-48_5_1_0_aq

description: untreated


title: trtA-48_5_1_0_av

description: untreated


title: Liver tissue at day 14, biological replication ID J14


title: Liver tissue at day 1, biological replication ID J80


title: trt-24_3_1_0_ao

description: untreated


title: Liver tissue at day 3, biological replication ID 32


title: trt-24_4_0_1_al

description: inactive cyclophosphamide

source_name: PC-3 inactive compound 24 hours


title: Liver tissue at day 0, biological replication ID J40


title: trt-24_3_1_0_ai

description: untreated


title: Liver tissue at day 0, biological replication ID N6


title: trt-24_4_0_1_ap

description: inactive cyclophosphamide


title: trt-10_2_0_1_an

description: inactive cyclophosphamide

source_name: PC-3 inactive compound 10 hours


title: trt-10_1_1_0_am

description: untreated


title: Liver tissue at day 42, biological replication ID J55


title: trt-24_3_1_0_ac

description: untreated


title: Liver tissue at day 14, biological replication ID J47


title: trt-24_4_0_1_ad

description: inactive cyclophosphamide


title: trt-48_5_1_0_ae

description: untreated


title: Liver tissue at day 21, biological replication ID J3


title: Liver tissue at day 21, biological replication ID N26


title: Liver tissue at day 42, biological replication ID N20


title: Spleen leukocytes_C57BL/6 mice_4wk_rep 4 [430A]

city: Memphis

first: Dorothy

middle: N.

last: Kakoola

state: TN

address: 1030 Jefferson Avenue

department: Medicine

institute: University of Tennessee Health Science Center

description: Gene expression data from ex vivo untreated spleen leukocytes of 4 week-old mice.

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

source_name: Spleen leukocytes collected from 4 wk-old C57BL/6 mice

growth_protocol: Spleen leukocytes were uncultured

treatment_protocol: Spleen leukocytes were untreated

value: untreated ex vivo Spleen leukocytes

value: C57BL/6 mice

tag: age

value: 4 week


title: Liver tissue at day 14, biological replication ID N98

source_name: Mouse Liver tissue after 14 days of caloric restriction


title: Spleen leukocytes_C57BL/6 mice_4wk_rep 2 [430A]


title: Liver tissue at day 3, biological replication ID N90

source_name: Mouse Liver tissue after 3 days of caloric restriction


title: Liver tissue at day 1, biological replication ID J7


title: Liver tissue at day 42, biological replication ID N37


title: Liver tissue at day 7, biological replication ID N97


title: trt-10_1_1_0_ag

description: untreated


title: Liver tissue at day 42, biological replication ID J33


title: Liver tissue at day 60, biological replication ID N14


title: trt-10_1_1_0_aa

description: untreated

data_processing: Transcript average-intensity signals were calculated with BeadStudio without background correction. Raw data were analyzed using Bioconductor (R 2.12.0, Bioconductor 2.7, oneChannelGUI 1.16.5). Average transcript intensities were log2 transformed and normalized by loess method.


title: trt-10_2_0_1_ab

description: inactive cyclophosphamide


title: trt-48_6_0_1_af

description: inactive cyclophosphamide


title: trt-10_2_0_1_ah

description: inactive cyclophosphamide


title: Liver tissue at day 3, biological replication ID J16


title: Spleen leukocytes_C57BL/6 mice_4wk_rep 5 [430A]


title: Liver tissue at day 60, biological replication ID N43


title: Liver tissue at day 21, biological replication ID J91

source_name: Mouse Liver tissue after 21 days of caloric restriction


title: Spleen leukocytes_C57BL/6 mice_4wk_rep 3 [430A]


title: Spleen leukocytes_NON mice_4wk_rep 4 [430A]

source_name: Spleen leukocytes collected from 4 wk-old NON mice

value: NON mice


title: Liver tissue at day 42, biological replication ID J36


title: Liver tissue at day 0, biological replication ID J5

source_name: Mouse Liver tissue after 0 days of caloric restriction


title: Spleen leukocytes_NON mice_4wk_rep 5 [430A]


title: Liver tissue at day 3, biological replication ID N2


title: Liver tissue at day 14, biological replication ID J51


title: Liver tissue at day 42, biological replication ID J30

source_name: Mouse Liver tissue after 42 days of caloric restriction


title: Liver tissue at day 0, biological replication ID J43


title: Spleen leukocytes_C57BL/6 mice_4wk_rep 1 [430A]


title: Liver tissue at day 7, biological replication ID N0

source_name: Mouse Liver tissue after 7 days of caloric restriction


title: Spleen leukocytes_NON mice_4wk_rep 2 [430A]


title: Spleen leukocytes_NOD mice_4wk_rep 5 [430A]

source_name: Spleen leukocytes collected from 4 wk-old NOD mice

value: NOD mice


title: Liver tissue at day 21, biological replication ID N99


title: Liver tissue at day 21, biological replication ID N91


title: Spleen leukocytes_NOD mice_4wk_rep 2 [430A]


title: Spleen leukocytes_NOD mice_4wk_rep 3 [430A]


title: Spleen leukocytes_C57BL/6 mice_2wk_rep 5 [430A]

description: Gene expression data from ex vivo untreated spleen leukocytes of 2 week-old mice.

source_name: Spleen leukocytes collected from 2 wk-old C57BL/6 mice

value: 2 week


title: Liver tissue at day 42, biological replication ID J4

value: Male


title: Liver tissue at day 42, biological replication ID N10


title: Spleen leukocytes_NON mice_4wk_rep 3 [430A]


title: Spleen leukocytes_NOD mice_4wk_rep 1 [430A]


title: Spleen leukocytes_NON mice_4wk_rep 1 [430A]


title: Spleen leukocytes_NOD mice_4wk_rep 4 [430A]


title: Liver tissue at day 3, biological replication ID J11


title: Spleen leukocytes_C57BL/6 mice_2wk_rep 3 [430A]


title: Spleen leukocytes_C57BL/6 mice_2wk_rep 4 [430A]


title: Spleen leukocytes_C57BL/6 mice_2wk_rep 2 [430A]


title: Liver tissue at day 3, biological replication ID N13


title: Spleen leukocytes_C57BL/6 mice_2wk_rep 1 [430A]


title: Liver tissue at day 7, biological replication ID J44


title: Hypothalamus tissue at day 42, biological replication ID J55

source_name: Mouse Hypothalamus tissue after 42 days of caloric restriction

value: Hypothalamus


title: Spleen leukocytes_NON mice_2wk_rep 2 [430A]

source_name: Spleen leukocytes collected from 2 wk-old NON mice


title: Spleen leukocytes_NON mice_2wk_rep 1 [430A]


title: Spleen leukocytes_NON mice_2wk_rep 5 [430A]


title: Hypothalamus tissue at day 21, biological replication ID J2

source_name: Mouse Hypothalamus tissue after 21 days of caloric restriction


title: Hypothalamus tissue at day 42, biological replication ID N69


title: Liver tissue at day 21, biological replication ID N80


title: Hypothalamus tissue at day 21, biological replication ID N91


title: Spleen leukocytes_NOD mice_2wk_rep 1 [430A]

source_name: Spleen leukocytes collected from 2 wk-old NOD mice


title: Spleen leukocytes_NOD mice_2wk_rep 2 [430A]


title: Hypothalamus tissue at day 21, biological replication ID J3


title: Hypothalamus tissue at day 7, biological replication ID N16

source_name: Mouse Hypothalamus tissue after 7 days of caloric restriction


title: Spleen leukocytes_NOD mice_2wk_rep 4 [430A]


title: Spleen leukocytes_NON mice_2wk_rep 4 [430A]


title: Hypothalamus tissue at day 0, biological replication ID J5

source_name: Mouse Hypothalamus tissue after 0 days of caloric restriction


title: Hypothalamus tissue at day 60, biological replication ID N82

source_name: Mouse Hypothalamus tissue after 60 days of caloric restriction


title: Spleen leukocytes_NON mice_2wk_rep 3 [430A]


title: Spleen leukocytes_NOD mice_2wk_rep 3 [430A]


title: Hypothalamus tissue at day 3, biological replication ID N12

source_name: Mouse Hypothalamus tissue after 3 days of caloric restriction


title: Hypothalamus tissue at day 7, biological replication ID N15


title: Hypothalamus tissue at day 0, biological replication ID N74


title: Spleen leukocytes_NOD mice_2wk_rep 5 [430A]


title: Hypothalamus tissue at day 21, biological replication ID N3


title: Spleen leukocytes_C57BL/6 mice_4wk_rep 5 [430B]

source_name: Spleen leukocytes collected from 4 wk-old C57BL/6 mice


title: Hypothalamus tissue at day 21, biological replication ID J91


title: Spleen leukocytes_C57BL/6 mice_4wk_rep 1 [430B]


title: Spleen leukocytes_C57BL/6 mice_4wk_rep 3 [430B]


title: Spleen leukocytes_NON mice_4wk_rep 4 [430B]


title: Spleen leukocytes_NON mice_4wk_rep 2 [430B]


title: Hypothalamus tissue at day 1, biological replication ID J20

source_name: Mouse Hypothalamus tissue after 1 days of caloric restriction


title: Spleen leukocytes_NON mice_4wk_rep 3 [430B]


title: Spleen leukocytes_C57BL/6 mice_4wk_rep 4 [430B]


title: Spleen leukocytes_C57BL/6 mice_4wk_rep 2 [430B]


title: Hypothalamus tissue at day 3, biological replication ID J16


title: Hypothalamus tissue at day 21, biological replication ID J10


title: Hypothalamus tissue at day 0, biological replication ID N6


title: Spleen leukocytes_NON mice_4wk_rep 5 [430B]


title: Hypothalamus tissue at day 14, biological replication ID N35

source_name: Mouse Hypothalamus tissue after 14 days of caloric restriction


title: Spleen leukocytes_NOD mice_4wk_rep 5 [430B]


title: Spleen leukocytes_NON mice_4wk_rep 1 [430B]

source_name: Spleen leukocytes collected from 4 wk-old NON mice


title: Hypothalamus tissue at day 42, biological replication ID N37


title: Hypothalamus tissue at day 0, biological replication ID J42


title: Hypothalamus tissue at day 21, biological replication ID N26


title: Spleen leukocytes_NOD mice_4wk_rep 4 [430B]


title: Hypothalamus tissue at day 42, biological replication ID J33


title: Spleen leukocytes_NOD mice_4wk_rep 2 [430B]


title: Spleen leukocytes_NOD mice_4wk_rep 1 [430B]


title: Hypothalamus tissue at day 14, biological replication ID J51


title: Spleen leukocytes_C57BL/6 mice_2wk_rep 5 [430B]


title: Hypothalamus tissue at day 7, biological replication ID N0


title: Hypothalamus tissue at day 60, biological replication ID N43


title: Spleen leukocytes_C57BL/6 mice_2wk_rep 1 [430B]


title: Spleen leukocytes_C57BL/6 mice_2wk_rep 3 [430B]


title: Hypothalamus tissue at day 3, biological replication ID N2


title: Hypothalamus tissue at day 42, biological replication ID N10


title: Spleen leukocytes_NOD mice_4wk_rep 3 [430B]


title: Spleen leukocytes_C57BL/6 mice_2wk_rep 4 [430B]


title: Spleen leukocytes_NON mice_2wk_rep 4 [430B]


title: Hypothalamus tissue at day 7, biological replication ID N39


title: Hypothalamus tissue at day 14, biological replication ID N98


title: Spleen leukocytes_NON mice_2wk_rep 3 [430B]


title: Hypothalamus tissue at day 3, biological replication ID 32


title: Spleen leukocytes_NON mice_2wk_rep 2 [430B]


title: Hypothalamus tissue at day 1, biological replication ID J15


title: Spleen leukocytes_NON mice_2wk_rep 5 [430B]


title: Spleen leukocytes_C57BL/6 mice_2wk_rep 2 [430B]


title: Spleen leukocytes_NOD mice_2wk_rep 5 [430B]


title: Spleen leukocytes_NON mice_2wk_rep 1 [430B]


title: Hypothalamus tissue at day 7, biological replication ID J22


title: Hypothalamus tissue at day 60, biological replication ID N59


title: Hypothalamus tissue at day 0, biological replication ID N72


title: Spleen leukocytes_NOD mice_2wk_rep 1 [430B]


title: Hypothalamus tissue at day 0, biological replication ID N45


title: E. coli 2h_rep2

city: Starkville

first: Minny

last: Bhatty

state: Mississippi

address: 240 Wise Center Dr, Mississippi State

institute: Mississippi State University

description: Peritoneal lavage fluid was isolated 2h after intraperitoneal inoculation of E. coli

hyb_protocol: Following fragmentation, 10 µg cRNA were hybridized for 16 hr at 45° C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data was normalized by using the Robust Multichip Average (RMA) protocol implemented in Genesifter (Geospiza, Seattle, WA)

label: Biotin

source_name: Peritoneal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from approximately 7.5 µg total RNA using the GeneChip IVT Labeling Kit (Affymetrix)  Biotinylated cRNA were prepared according to the standard Affymetrix protocol from approximately 7.5 ug total RNA using the GeneChip IVT Labeling Kit (Affymetrix)

extract_protocol: RNA was extracted from peritoneal cells using TRIzol (Invitrogen, Stockholm, Sweden) protocol

treatment_protocol: Each mice in the E. coli infected group was injected with a 2X108 cells of a non-pathogenic strain of E. coli intraperitoneally, the control group was injected with an equal amount of PBS. Peritonal lavage fluid was obtained from each mice 1, 2 and 18 h after infection

value: female

value: C57Bl/6 x C3H F1


title: Hypothalamus tissue at day 1, biological replication ID J60


title: Hypothalamus tissue at day 14, biological replication ID J47


title: E. coli 18h_rep1

description: Peritoneal lavage fluid was isolated 1h after intraperitoneal inoculation of E. coli


title: E. coli 1h_rep2

value: Peritoneal lavage fluid was isolated 1h after intraperitoneal inoculation of E. coli


title: Hypothalamus tissue at day 42, biological replication ID N20


title: Spleen leukocytes_NOD mice_2wk_rep 2 [430B]


title: Spleen leukocytes_NOD mice_2wk_rep 4 [430B]


title: Hypothalamus tissue at day 14, biological replication ID N33


title: E. coli 1h_rep1


title: E. coli 18h_rep3

description: Peritoneal lavage fluid was isolated 18h after intraperitoneal inoculation of E. coli


title: Hypothalamus tissue at day 3, biological replication ID J9


title: E. coli 18h_rep2

value: Peritoneal lavage fluid was isolated 18h after intraperitoneal inoculation of E. coli


title: Hypothalamus tissue at day 21, biological replication ID N99


title: Hypothalamus tissue at day 60, biological replication ID N22


title: Hypothalamus tissue at day 21, biological replication ID N11


title: Spleen leukocytes_NOD mice_2wk_rep 3 [430B]


title: Naïve 18h_rep2

description: Peritoneal lavage fluid was isolated 18h after intraperitoneal inoculation of PBS


title: CL1-5 24h 1/25

first: Mong-Hsun

last: Tsai

address: 4F, No. 81, Chang-Xing St.

department: Institute of Biotechnology

institute: National Taiwan University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization were carried out using Partek microarray analysis software.

source_name: IR 24h

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

growth_protocol: Culture with RPMI medium

extract_protocol: Total RNA from the cells were isolated using TRIzol® reagent (Invitrogen, Calsbad, CA) and purified with RNeasy® mini kits (Qiagen)

treatment_protocol: irradiation

value: lung adenocarcinoma

tag: treatment

value: 10 Gy radiation

tag: harvest time after exposure


title: CL1-5 4h 1/25

source_name: IR 4h


title: CL1-5 1h 1/25

source_name: IR 1h


title: CL1-0 24h 1/25


title: CL1-5 0h 1/25

source_name: IR 0h


title: Naïve 1 and 2h_rep1

description: Peritoneal lavage fluid was isolated 2h after intraperitoneal inoculation of PBS


title: Naïve 18h_rep3

value: Peritoneal lavage fluid was isolated 18h after intraperitoneal inoculation of PBS


title: CHUB-S7, B12-0nM, folate-60uM; 3

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

institute: The Genome Analysis Centre

description: Sample 12

hyb_protocol: The labelled cRNAs were hybridised to SurePrint G3 Human Gene Expression 8x60K Gene Expression arrays (AMADID 028004; Agilent Technologies) according to the manufacturer's instructions. The arrays were washed in Gene Expression Wash Buffer 1 and Gene Expression Wash Buffer 2.

scan_protocol: Immediately after washing, the arrays were scanned in an Agilent GA2565CA scanner at 2µm resolution.

data_processing:
The data were extracted using Feature Extraction v10.7.3.1 with default settings appropriate to the array design.
Normalisation and initial analysis of raw microarray data were carried out using GeneSpring GX (Grewal and Conway, 2000) software. Signal values were thresholded to a value of 5, normalised to 75th percentile, baseline transformed to median of all samples, and log-transformed. Array quality metrics, and Principal Components Analysis (PCA) of expression by condition, were assessed and one outlier array removed. Normalisation was repeated on the remaining arrays. One-way ANalysis Of VAriance (ANOVA) was carried out to assess significant differences in probe intensity between conditions. Probes with p < 0.05 after correction for multiple testing were regarded as having significantly different log intensity between conditions. The Normal B12, Normal folate condition was used as a control treatment, and probes whose log intensity in other conditions was significantly different, and whose fold change was > 2 between another condition and the control, were regarded as Differentially Expressed Genes (DEGs) for subsequent analysis.

source_name: CHUB-S7, no B12, 60uM folate

label_protocol: The RNA concentrations were normalised to 100ng in 1.5µL and the Low Input QuickAmp Labelling Kit Protocol (Agilent Technologies) was followed according to the manufacturer's instructions. All of the samples were labelled in randomised batches with Cyanine 3-CTP, and yields and specific activities were within the recommended ranges.

growth_protocol: The human pre-adipocyte cell line CHUB-S7 was cultured and differentiated similarly to primary human pre-adipocytes as described elsewhere (15). Briefly, the pre-adipocytes were grown in 6-well plates to confluence in customised DMEM/Ham's F-12 medium containing 10% fetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100 µg/ml), and transferrin (5 µg/ml). At confluence, pre-adipocytes were differentiated in differentiation media containing DMEM/Ham's F-12 phenol-free medium containing biotin (8 μg/ml), insulin (500 ng/ml), dexamethasone (400 ng/ml), IBMX (44 μg/ml), L-Thyroxin (9ng/ml) and Ciglitazone (3μg/ml) for 72 hours. After 72 hours, the differentiating cells were grown in nutrition media containing DMEM/Ham's F-12 phenol-free medium containing 3% FCS, d-biotin (8 μg/ml), insulin (500 ng/ml) and dexamethasone (400 ng/ml) until the cells are fully differentiated (10-14 days). Media were changed every 48hrs. Cells were harvested by scraping, snap frozen and stored at -80oC until use. Conditioned media was collected on the day of harvesting, snap frozen and stored at -80oC until use.

extract_protocol: The total RNA from the adipocytes was isolated using the RNeasy Lipid Tissue Mini Kit (Qiagen, UK) according to the manufacturer's protocol. Total RNA samples were quality checked on an Agilent Bioanalyser 1200 (Agilent Technologies, Inc., Santa Clara, CA, USA) and RNA Integrity Numbers between 6.5 and 9.8 were obtained.

treatment_protocol: The DMEM/Ham's F-12 medium used for growth as well as for differentiation was customised for folate and B12 concentrations. The pre-adipocytes were cultured in different B12 (0-50uM) and folate (0-60μM) concentrations from the day of cell seeding till harvesting. The media was customised for four different B12 and folate concentrations and hereafter referred throughout the manuscript as: (1) Control: (B12 - 500nM, folate-6uM); (2) No B12/High folate: (B12 - 0nM, folate - 0, 30, 60uM); and (4) High B12/No folate : (B12 - 50uM, folate - 0). The different B12/folate concentrations had no significant effect on cell viability and there were no obvious differences in cell morphology.

value: adipocyte cells

tag: b12 treatment

tag: folate treatment


title: Hypothalamus tissue at day 3, biological replication ID J11

tag: gender


title: Hypothalamus tissue at day 0, biological replication ID J40

tag: strain


title: E. coli 2h_rep1

value: Peritoneal lavage fluid was isolated 2h after intraperitoneal inoculation of E. coli


title: CL1-0 0h 1/25


title: CL1-0 4h 1/25


title: CL1-0 1h 1/25


title: CHUB-S7, B12-50uM, folate-0uM; 2

description: Sample 14

source_name: CHUB-S7, 50uM B12, no folate

tag: cell type


title: CHUB-S7, B12-0nM, folate-60uM; 2

description: Sample 11


title: CHUB-S7, B12-500nM, folate-6uM; 4

description: Sample 16

source_name: CHUB-S7, 500nM B12, 6uM folate


title: Naïve 18h_rep1


title: Naïve 1 and 2h_rep2

value: Peritoneal lavage fluid was isolated 2h after intraperitoneal inoculation of PBS


title: CL1-5 24h 12/24


title: CHUB-S7, B12-50uM, folate-0uM; 3

description: Sample 15


title: Hypothalamus tissue at day 3, biological replication ID J23


title: CL1-5 1h 12/24


title: CHUB-S7, B12-0nM, folate-30uM; 1

description: Sample 7

source_name: CHUB-S7, no B12, 30uM folate


title: Hypothalamus tissue at day 14, biological replication ID J14


title: CHUB-S7, B12-50uM, folate-0uM; 1

description: Sample 13


title: CHUB-S7, B12-0nM, folate-30uM; 2

description: Sample 8


title: CHUB-S7, no B12, no folate; 2

description: Sample 5

source_name: CHUB-S7, no B12, no folate


title: CHUB-S7, B12-0nM, folate-30uM; 3

description: Sample 9


title: CHUB-S7, no B12, no folate; 3

description: Sample 6


title: Hypothalamus tissue at day 42, biological replication ID J4

source_name: Mouse Hypothalamus tissue after 42 days of caloric restriction


title: Hypothalamus tissue at day 60, biological replication ID N14

source_name: Mouse Hypothalamus tissue after 60 days of caloric restriction


title: Hypothalamus tissue at day 7, biological replication ID J25

source_name: Mouse Hypothalamus tissue after 7 days of caloric restriction


title: CL1-5 4h 12/24


title: Hypothalamus tissue at day 42, biological replication ID J21


title: Hypothalamus tissue at day 21, biological replication ID J8

source_name: Mouse Hypothalamus tissue after 21 days of caloric restriction


title: CHUB-S7, B12-500nM, folate-6uM; 3

description: Sample 3


title: CL1-0 24h 12/24


title: CL1-5 0h 12/24


title: CL1-0 0h 12/24


title: CL1-0 1h 12/24


title: CL1-5 24h 8/26


title: CL1-5 1h 8/26


title: CL1-5 0h 8/26


title: CL1-0 24h 8/26


title: CL1-5 4h 8/26


title: CL1-0 4h 8/26


title: CL1-0 0h 8/26


title: CL1-0 1h 8/26


title: CHUB-S7, no B12, no folate; 1

description: Sample 4


title: Hypothalamus tissue at day 42, biological replication ID N92


title: GILs_Allogeneic_Day5_3

city: Stanford

first: Liang

last: Wei

address: 1201 Welch Rd MSLS P328

department: Surgery

institute: Stanford University

description: Allo GILs 3

data_processing: Data was analyzed using SDS and RQ software (Applied Biosystems). Fold changes for each miRNA were normalized to the endogenous control snoRNA202. The relative expression levels were calculated using the 2-∆∆Ct method. For heart grafts, normal BALB/c hearts were used as a calibrator. For GILs, normal C57BL/6 PBMC was used as a calibrator.

label: FAM

source_name: 3 pooled allogeneic GILs_Day 5 post Tx

label_protocol: The PCR reaction was carried out on an Applied BioSystems 7900HT thermocycler.

growth_protocol: Eight to ten-week-old C57BL/6 and BALB/c mice were used. Syngeneic (C57BL/6 to C57BL/6) and allogeneic (BALB/c to C57BL/6) heterotopic heart transplants were performed.

extract_protocol: Total RNA was isolated from heart grafts, GILs and PBLs using the mirVana miRNA isolation kit (Applied Biosystems, Foster City, CA). Total RNA isolated from hearts of normal BALB/c mice (donor) and PBLs of normal C57BL/6 (recipient) mice were used as controls and calibrators for microarray data analysis. Three individual RNA samples from either transplanted or normal animals were pooled together (100 ng of each, 300 ng in total) for cDNA preparation using TaqMan microRNA reverse transcription kit and the corresponding Megaplex primer pools (Applied Biosystems). The resulting cDNA samples underwent preamplification using TaqMan PreAmp master mix and corresponding Megaplex PreAmp primers (Applied Biosystems).

tag: donor

value: Allogeneic

value: BALB/c to C57BL/6

tag: rejection

value: Yes


title: PB-MCs rep1

city: Tsukuba

first: Hisako

last: Ishimine

state: Japan Ibaraki

address: higashi1-1-1 Tsukuba central 4

department: Research Center for Stem Cell Engineering

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression of PB-MCs

hyb_protocol: 0.4 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), and 30 second at room temperature with acetonitrile,  then dried immediately.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20101102 ) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non positive and significant, and Feature Non above background outliers were excluded.

source_name: human peripheral blood derived monocytes

label_protocol: RNA was labeled using the ‘Agilent Quick-Amp Labeling Kit’ (Agilent Technologies) following the manufacturer’s protocol. Cy3-labeled cRNA was purified with the RNeasy kit (Qiagen). Dye incorporation was assessed with the NanoDrop-1000 Spectrophotometer.

growth_protocol: Liposuction aspirates were obtained from healthy donors undergoing liposuction of the abdomen and thighs.the aspirated fat was washed with phosphate-buffered saline (PBS) and digested on a shaker at 37℃ in PBS containing 0.075% collagenase for 30 minutes. Mature adipocytes and connective tissue were separated from pellets by centrifugation. Peripheral blood was obtained from healthy volunteers.

extract_protocol: Total RNA were isolated from each samples using ISOGEN (Nippon Gene) according to the manufactureres’ recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: CD34-positive AT resident macrophages (ATMs), CD34-negative ATMs and adipose stromal cells were isorted from aspirated AT by a multiparameter fluorescent-activated cell sorter. Circulating monocytes were also sorted from peripheral blood.

value: peripheral blood derived monocytes


title: CHUB-S7, B12-500nM, folate-6uM; 1

description: Sample 1

tag: cell line


title: Hypothalamus tissue at day 60, biological replication ID N62

tag: tissue


title: PBMC_Normal_Control

description: Normal PBMC

source_name: 3 pooled normal PBMC of C57BL/6 mice


title: Hypothalamus tissue at day 21, biological replication ID N80


title: GILs_Allogeneic_Day5_1

description: Allo GILs 1


title: GILs_Syngeneic_Day5_3

description: Syn GILs 3

source_name: 3 pooled syngeneic GILs_Day 5 post Tx

value: Syngeneic

value: C57BL/6 to C57BL/6

value: No


title: GILs_Syngeneic_Day5_2

description: Syn GILs 2


title: Hypothalamus tissue at day 7, biological replication ID J6

value: Male

value: Hypothalamus


title: ASC rep1

description: Gene expression of ASCs

source_name: human adipose derived stem cells

value: adipose derived stem cells


title: Hypothalamus tissue at day 0, biological replication ID J17

source_name: Mouse Hypothalamus tissue after 0 days of caloric restriction


title: ATM CD34(-) rep1

description: Gene expression of CD34(-) ATMs

source_name: human adipose tissue resident macropgages, CD34(-)


title: ATM CD34(+) rep1

description: Gene expression of CD34(+) ATMs

source_name: human adipose tissue resident macropgages, CD34(+)


title: Hypothalamus tissue at day 14, biological replication ID J13

source_name: Mouse Hypothalamus tissue after 14 days of caloric restriction


title: Hypothalamus tissue at day 7, biological replication ID J52


title: Hypothalamus tissue at day 3, biological replication ID N13

source_name: Mouse Hypothalamus tissue after 3 days of caloric restriction


title: Hearts_Normal_Control

description: Normal hearts

source_name: 3 pooled normal hearts of BALB/c mice

value: Balb/c


title: GILs_Syngeneic_Day5_1

description: Syn GILs 1


title: Hypothalamus tissue at day 7, biological replication ID J34


title: GILs_Allogeneic_Day5_2

description: Allo GILs 2


title: Heart grafts_Allogeneic_Day7_3

description: Allo heart grafts 3

source_name: 3 pooled allogeneic heart grafts_Day 7 post Tx


title: Heart grafts_Syngeneic_Day7_3

description: Syn heart grafts 3

source_name: 3 pooled syngeneic heart grafts_Day 7 post Tx


title: Heart grafts_Syngeneic_Day7_2

description: Syn heart grafts 2


title: Heart grafts_Syngeneic_Day7_1

description: Syn heart grafts 1


title: Heart grafts_Allogeneic_Day7_2

description: Allo heart grafts 2


title: Hypothalamus tissue at day 14, biological replication ID J26


title: Hypothalamus tissue at day 14, biological replication ID N93


title: Hypothalamus tissue at day 21, biological replication ID J1


title: Heart grafts_Allogeneic_Day7_1

description: Allo heart grafts 1


title: Hypothalamus tissue at day 0, biological replication ID N30


title: Hypothalamus tissue at day 14, biological replication ID J57


title: Hypothalamus tissue at day 0, biological replication ID N50


title: Hypothalamus tissue at day 1, biological replication ID J80

source_name: Mouse Hypothalamus tissue after 1 days of caloric restriction


title: Hypothalamus tissue at day 42, biological replication ID J36

source_name: Mouse Hypothalamus tissue after 42 days of caloric restriction


title: Hypothalamus tissue at day 3, biological replication ID J12


title: Hypothalamus tissue at day 42, biological replication ID N70


title: Hypothalamus tissue at day 7, biological replication ID N44

source_name: Mouse Hypothalamus tissue after 7 days of caloric restriction


title: Hypothalamus tissue at day 1, biological replication ID J7


title: hESCs-derived CXCR4+/CD61-,  biological rep2

status: Public on Dec 29 2012

city: Rehovot

first: Yoav

last: Soen

address: Department of Biological Chemistry, Weizmann Institute of Science

country: Israel

institute: Weizmann Institute of Science

description:
CXCR4+/CD61-_2
hESCs-derived early endoderm sub-population of CXCR4+/CD61- cells

hyb_protocol: GeneChip (Affymetrix) human genome ST1 series arrays were used. Sample preparation, array hybridization, array washing and scanning were performed according to the manufacturer's protocol.

scan_protocol: Data from the individual arrays were acquired using  Affymetrix 7G and Expression Console software.

data_processing:
Data from the individual arrays were analyzed using GCOS software. Expression values were normalized by Expression Console software using robust multi-array average (RMA) algorithm.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.na31.hg19.transcript.csv

label: PE

label_protocol: Staining of cells was carried out in PBS containing 3% FBS using the following antibodies: PE conjugated anti-CXCR4, anti-CD61, and Alexa fluor 647 as secondary antibody. We used propidium iodide (Biotium) at 2µg/ml to mark dead cells.

growth_protocol: HUES-2 and H9 hES cell lines were cultured essentially as described (Cowan et al., 2004). In brief, cells were cultured on irradiated ICR MEF feeder cells in DMEM/F-12 (HAM) (Invitrogen), supplemented with 15% KnockOut Serum Replacement (Invitrogen),  0.1 mM 2-mercaptoethanol (Invitrogen), 0.1mM MEM nonessential amino acids (Invitrogen), 1 × P/S L-glutamine  (Invitrogen), and 8 ng/ml bFGF (Peprotech). Cells were split at the ratio of 1:3 every 3–4 days using 1 mg/ml collagenase type IV (Worthington).

extract_protocol: Cells were dissociated and filtered through 40µm nylon strainer (BD Falcon), then sorted by FACSAria flow cytometer (BD).

treatment_protocol: Stage 1 differentiation as described by Kroon et al. (Kroon E, Martinson LA, Kadoya K, et al. Pancreatic endoderm derived from human embryonic stem cells generates glucose-responsive insulin-secreting cells in vivo. Nat Biotechnol. 2008;26:443-452.)

tag: source


title: mesenchymal stem cells, lot#7032R, 2th passage

city: Los Angeles

first: Lingtao

last: Wu

address: 4650 Sunset Blvd.

department: Children hispotial of Los angeles, Dept. of Pathology, MS# 103

institute: University of Southern California

description: Gene expression data from bone marrow mesenchymal stem cells.Cells were purchased from TUCGT (Tulane University Center for Gene Therapy) under material transfer agreement. Cells were cultured according to manufacturer's protocol.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for aprx. 16 hr at 45℃ on Affymetrix human genome HG-U133A genechip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanned on a GeneArray scanner.

data_processing: The data were analyzed using GCOS Affymetrix standard analysis settings and mask-file (Affymetrix, hgu133_plus_2norm) scaling as normalization methods. The trimmed mean target intensity of each array was arbitrarily set to 10000. dChip was used for probe set summarization.

source_name: mesenchymal stem cells, lot# 7032R, 2th passage

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

growth_protocol: Cells were cultured according to manufacturer's protocol. Cells were grown at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA extraction was performed using silica-membrane RNeasy spin columns according to manufacturer's protocol (QIAGEN, RNeasy)

treatment_protocol: Cells were lysed in 600 ul of buffer RLT (QIAGEN).

value: bone marrow mesenchymal stem cells


title: hESCs-derived CXCR4+,  biological rep2

description:
CXCR4+_2
hESCs-derived early endoderm population of CXCR4+ cells

value: hESCs-derived early endoderm population


title: osteosarcoma U2OS cells

description:
Gene expression data from human osteosarcoma U2OS cells. Cells were maintained in RPMI 1640 (Gibco, 2 g/l glucose) with 10% fetal calf serum (NCS, Gibco) plus 2 mmol/l glutamine and 50 U/ml penicillin.
Organ: bone; Disease: osteosarcoma; Age: 15 years; Gender: female; Comments: J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma of the tibia of a 15 year old girl.

source_name: The total RNA from osteosarcoma cell line U2OS

value: osteosarcoma U2OS cells


title: hESCs-derived CD61+,  biological rep2

description:
CD61+ _2
hESCs-derived early endoderm sub-population of CD61+ cells

label: Alexa Fluor 647


title: hESCs-derived CD61+,  biological rep1

description:
CD61+ _1
hESCs-derived early endoderm sub-population of CD61+ cells


title: Hypothalamus tissue at day 42, biological replication ID J30


title: osteosarcoma U2OS derived cell line UT2

description:
Gene expression data from human osteosarcoma UT2 cells.Cells were maintained in RPMI 1640 (Gibco, 2 g/l glucose) with 10% fetal calf serum (NCS, Gibco) plus 2 mmol/l glutamine and 50 U/ml penicillin.
Derived from the second human–mouse xenotransplantation of U2OS cell-formed osteosarcoma tissues.

source_name: The total RNA from osteosarcoma U2OS derived cell line-UT2

value: osteosarcoma U2OS derived cell line UT2


title: pooled plasma of CRCs

city: Shanghai

first: Qifeng

address: NO 270,Dongan Road

country: China

institute: Cancer Hospital, Fudan University

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions
For the normalization it uses the average of six reference genes
TargetmiRNA signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
deltadeltaCt based fold-changes were calculatd from the uploaded raw threshold cycle data.
Matrix  non-normalized data reports the raw Ct values. Ct values of some  undetermined wells were uniformlly  calculated as 40.
Matrix normalized worksheet reports normalized signal (against housekeeping miRNAs).
Fold Change worksheet reports test/control  ratios.

label: SYBR Green

source_name: plasma

label_protocol: PCR assays were performed using the microRNA Ready-to-Use PCR human panel I+II (Exiqon, Demark) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the Universal cDNA Synthesis Kit (Exiqon, Demark). Quantitative real-time PCR were performed (7900HT,ABI) with 40 cycles at 95 oC for 10 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with MirVana PARIS Kit (Ambion, USA).

value: pooled plasma

tag: disease status

value: CRC


title: pooled plasma of healthy control

description: Control

value: healthy control


title: hESCs-derived CXCR4+, biological rep1

description:
CXCR4+_1
hESCs-derived early endoderm population of CXCR4+ cells


title: CL1-0 4h 12/24

source_name: IR 4h

value: lung adenocarcinoma

value: 10 Gy radiation


title: KYSE30 transfected with siRNA combination

city: Beijing

first: Weidong

last: Han

address: #28 Fuxing Road, HaiDian District

department: School of Life Sciences

institute: Chinese PLA General Hospital

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R.

source_name: KYSE30 cells transfected with siRNA combination

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

growth_protocol: Grown in RPMI-1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: All cell groups were transfected using Lipofectamin2000 (Invitrogen) according to the manufacturer's instructions. 3 days post transfection cells were harvested for RNA extraction.

value: esophageal squamous cell carcinoma (ESCC)


title: KYSE30 transfected with miR-181a

source_name: KYSE30 cells transfected with miR-181a


title: KYSE30 transfected with siPIK3R3

source_name: KYSE30 cells transfected with siPIK3R3


title: KYSE30 transfected with miR-181b

source_name: KYSE30 cells transfected with miR-181b


title: KYSE30 transfected with miR-455

source_name: KYSE30 cells transfected with miR-455


title: Pancreatic islets_control_rep5

first: yanchang

last: wei

address: #1 Beichen West Rd

institute: Institute of Zoology, Chinese Academy of Sciences

description: This sample is the fifth of six control biological replicates used in this experiment, each from separate animals.

source_name: Pancreatic islets

growth_protocol: At 16 weeks of age, fathers of type 2 diabetes or control were mated with normal females in standard conditions, to generate the F1 offspring.

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

treatment_protocol: Fathers type 2 diabetes vs control, mate with females in standard conditions, then the offspring's liver transcriptomics were analysed through microarray analysis.

value: Female

value: ICR

value: Pancreatic islets

value: control


title: Pancreatic islets_t2d_rep2

description: This sample is the second of six experimental biological replicates used in this experiment, each from separate animals.

value: Male


title: Pancreatic islets_t2d_rep1

description: This sample is the first of six experimental biological replicates used in this experiment, each from separate animals.


title: Pancreatic islets_control_rep4

description: This sample is the fourth of six control biological replicates used in this experiment, each from separate animals.


title: KYSE30 transfected with miR-32

source_name: KYSE30 cells transfected with miR-32


title: Pancreatic islets_t2d_rep6

description: This sample is the last of six experimental biological replicates used in this experiment, each from separate animals.


title: KYSE30 transfected with siPIK3R1

source_name: KYSE30 cells transfected with siPIK3R1


title: Pancreatic islets_t2d_rep3

description: This sample is the third of six experimental biological replicates used in this experiment, each from separate animals.


title: CHUB-S7, B12-500nM, folate-6uM; 2

description: Sample 2

source_name: CHUB-S7, 500nM B12, 6uM folate

value: adipocyte cells


title: KYSE30 transfected with negative control

source_name: KYSE30 cells transfected with negative control


title: Pancreatic islets_t2d_rep4

description: This sample is the fourth of six experimental biological replicates used in this experiment, each from separate animals.


title: KYSE30 transfected with miRNA combination

source_name: KYSE30 cells transfected with miRNA combination


title: Pancreatic islets_control_rep2

description: This sample is the second of six control biological replicates used in this experiment, each from separate animals.