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However, since ChIP products are special subsets of the whole genome, extensive optimization of TTAS is required for its future application on ultralow cell number ChIP products.
This method offers an alternative to other previously published methods for low cell number ChIP-seq that entails fewer cycles of amplification with associated risk of data bias.
In line with the reviewer's comment we have now included a direct comparison of enrichments at control regions achieved using standard and low cell number ChIP protocol.
Increasing our stringency thresholds for SNPs in the WGS decreased the number chip loci that were present in the list of SNPs identified by sequencing (n = 329,690; ~78%), but increased concordance to ~95%.
To determine which genomic loci are marked by repressive histone methylation marks in vivo, the authors performed low cell number ChIP-seq assays for H3K27me3 and H3K9me2 in E6.25 epiblasts.
Both visual inspection and quantitative analyses of genomic coverage tracks from 10,000 cell ChIPs revealed good correspondence with libraries generated from biologically independent higher-cell-number ChIPs.
So they went around the room to every guest picker who had pulled a numbered chip out of a cup, piecing together the original order with help from the tiny screen on a photographer's camera.
We optimized the chromatin preparation procedure to ensure maximal input material for the small-cell-number ChIP (Additional file 8: Additional Protocols and Additional file 9: Figure S6).
CEBPA-1 peaks were to a high degree shared with a biological repeat (CEBPA −2), the diluted library (CEBPA-6) and the low-cell-number ChIP (CEBPA-10K) (Additional file 6: Additional Methods).
The signature length (also called chip rate) is defined as the number of chips in each signature code.
Histological examination was performed by one pathologist (MAR) for Gleason grade who also assessed tumour extent by calculating the ratio of the number of chips with cancer and the total number of chips (Humphrey and Vollmer, 1988).
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