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|Alternative name||Model-based Meta-analysis of ChIP data|
|Interface||Command line interface|
|Restrictions to use||None|
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- person_outline Liu Shirley
Publication for Model-based Meta-analysis of ChIP data
Sorting cells by their density
[…] ements in separation efficiency with increased channel length are fairly modest. To understand why, we used our density_sorter.py software to simulate the behavior of beads in the 8-turn channel (207 mm) chip. The simulation results () show that, as mentioned earlier, in fluid of uniform density the larger and less-dense polyethylene bead floats to the ceiling of the channel after only 1 mm of tra […]
Compact SAW aerosol generator
[…] zoelectric substrate, interdigital transducers (IDTs) and the polymer microchannel/s, all produced by conventional lift-off photolithography. On the chips used in this study (128°YX-LiNbO3, 8 mm × 19 mm chip size), pairs of IDTs (λ/4, λ = 90 μm, 46 finger pairs, 0.5 mm aperture, f0 ≅ 42.9 MHz) matched to 50 Ω impedance by design and consisting of subsequent layers of Ti (5 nm) and highly-textured […]
Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR γ
[…] e with the MACS version 1.4.1. Peaks of the methylation and hydroxymethylation datasets were determined similarly. For histone marks, MACS version two was used with parameters –broad, -q 0.01, and –g mm. ChIP-seq peaks were annotated using the annotatePeaks.pl script of the HOMER suite (version 4.6) () using the UCSC mm10 annotation. The coverage depths of different ChIP-seq experiments at specifi […]
RNA editing generates cellular subsets with diverse sequence within populations
[…] To generate single-cell libraries, wild-type bone marrow-derived macrophages were flowed into a C1 IFC for mRNA seq (10–17 μm) chip using the Fluigidm system. Lysis, RT and PCR were performed using the SMARTer Kit designed for the C1 (Clontech, Mountain View, CA). The efficiency of chip loading (capture) was confirmed by […]
A Detailed Protocol to Enable Safe Handling, Preemptive Detection, and Systematic Surveillance of Rat Vectored Pathogens in the Urban Environment
[…] ses, and connections for isoflurane unit. Isoflurane unit is on, all tubes connected. Table is clean. Instruments, microchips, and collection tubes on table.(2.3)Scan a selected microchip (Trovan® 12 mm chip is appropriate) to provide initial data point.(2.4)Place dry ice on two Pyrex 8″-roasting pans. One for ectorparasite collection and the other for body fluid collections. Anal swab (Swubes®) s […]
Urinary Kininogen 1 and Retinol binding protein 4 respond to Acute Kidney Injury: predictors of patient prognosis?
[…] formic acid in MilliQ water). A 6460 Triple Quadrupole mass spectrometer was used on-line connected to nano-chromatography in a Chip-format configuration (ChipCube interface, ProtID Zorbax 300B-C18-5 μm chip, 43 × 0.075-mm analytical column and 40 nL enrichment column, Agilent Technologies). The system was controlled by Mass Hunter Software (v4.0 Agilent Technologies). Theoretical SRM transitions […]
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