Results 41 to 50 of about 91 (71)
, 2020 Additional file 12. Repeat content analysis in GM02639 CT and KD MeDIP DNA shows subtle subfamily-specific methylation changes. CT and KD MeDIP repeat identification was performed as described for data in the Additional file 7. repeat identification and the occurrence of the three most populous repeats (Satellites, L1-LINEs and Alu-SINEs) were analyzed.
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, 2020 Additional file 1. Primer names, locations, sequences and annealing temperatures used for the candidate region methylation analyses shown in Additional file 14. The cyclic denaturation (95 °C, 30 s) and extension (70 °C) steps were the same for all primer combinations. Data was collected post-extension at 80 °C as mentioned in methods.
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, 2020 Additional file 10. The figure shows the methylation reads distribution in CT and KD at lower methylation bins (1 to 4) in GM02639 cells.
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, 2020 Additional file 13. Highly similar CTCF binding motifs are present in regions undergoing GoM, LoM or showing no methylation change upon CGGBP1 depletion. Methylation signals for CT and KD were calculated for each 0.2 kb bin for HEK293T and bins were grouped into GoM, LoM and “No change” (as described in method in details).
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, 2020 Additional file 4. Table represents GC content and percentage enrichment of CpG and non-CpG context cytosines in MeDIP read sequences for CT and KD in HEK293T and GM02639. The percentage of CpG, CHG and CHH represents the relative abundance for each cytosine context as a percentage of the total methylated cytosines enriched in MeDIP for CT and KD in ...
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, 2020 Additional file 2. CGGBP1 depletion in HEK293T cells: HEK293T cells were transduced with non-targeting shRNA or CGGBP1-targeting shRNA lentiviruses. Lentivirus-transduced cells were selected with 10 μg/ml Puromycin for 1 week and subjected to immunoblotting. The level of CGGBP1 and GAPDH are shown in the upper and lower panel respectively.
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, 2020 Additional file 6. The MeDIP signal correlation between CT and KD at different genomic bin sizes decline with a reduction in bin size specifically as randomization of coordinates (and thus corresponding sequences) changes the correlation stochastically away from the observed correlation coefficients with actual MeDIP sequences (refer to Additional file
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, 2020 Additional file 11. Raw data for Fig. 3k. A white light scan of the nuclear and cytoplasmic fractionation blot shows the molecular weight marker to the left. A dotted line between 26 kDa and 34 kDa bands indicates the line of incision at which the membrane was divided into two parts. As indicated, the top and the bottom parts were separately probed for
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, 2020 Additional file 8. Chemiluminescence scans of DBID blots shown in Fig. 3g. The well marked with a red X symbol contains a sample irrelevant to the experiments described. The antibodies used are indicated.
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, 2018 Additional file 1. A total of Tables S1 to S11 and Figures S1 to S7 with legends, details of methods and additional references are contained in the combined additional data file.
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