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| Status |
Public on Aug 11, 2023 |
| Title |
HepG2, nanoNOMe |
| Sample type |
SRA |
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| Source name |
HepG2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: Hepatocellular carcinoma
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| Treatment protocol |
GP5d cell nuclei was isolated and treated with GC methylase M.CviPI as described earlier (Sahu et al., Oncogene 2021).
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| Growth protocol |
GP5d cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was from GC methylated nuclei by using phenol chloroform extraction protocol.
NaNoME-seq library was prepared as described previously (Sahu et al., Oncogene 2021).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PromethION |
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| Data processing |
The GP5d nanopore data was basecalled with Guppy 5.0.17 with the super-accurate basecalling model and a minimum q-score of 10.
Basecalled reads were aligned to the reference genome with minimap2 2.16 (minimap2 –x map-ont –a).
Alignment and quality controls were performed with nanoplot 1.20.0 and Samtools 1.9.
After alignment, methylation was called with nanopolish v.0.11.1. The cpggpc_new_train branch (https://github.com/jts/nanopolish/tree/cpggpc_new_train) was used to call both CpG and GpC methylation (nanopolish call-methylation -q cpggpc).
The resulting table was processed to a BED format (mtsv2bedGraph.py -q cpggpc --nome) and to methylation frequency table formats for CpG and GpC methylation (parseMethylbed.py frequency -v -m cpg and parseMethylbed.py frequency -v -m gpc) with scripts from https://github.com/isaclee/nanopore-methylation-utilities
The resulting methylation tables were converted to bedGraph and bigwig formats with a self-made script (mfreq_to_bw.R), utilizing bedGraphToBigWig v377.
The CpG methylation frequency tables were loaded into R and smoothed with bsseq v.1.28.0 (BSmooth ns = 50, h = 1000, maxGap = 100000).
Assembly: hg38
Supplementary files format and content: Methylation frequency tables in in the same format as Bismark cytosine reports.
Library strategy: NaNoME-seq
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| Submission date |
Feb 03, 2023 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Konsta Karttunen |
| Organization name |
University of Helsinki
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| Street address |
Haartmaninkatu 8
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| City |
Helsinki |
| ZIP/Postal code |
00290 |
| Country |
Finland |
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| Platform ID |
GPL26167 |
| Series (2) |
| GSE221053 |
Transposable elements as lineage-specific enhancers in endodermal-lineage cancers |
| GSE224453 |
Transposable elements as lineage-specific enhancers in endodermal-lineage cancers [NaNoME-seq] |
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| Relations |
| BioSample |
SAMN32634916 |
| SRA |
SRX19013692 |
| SRA |
SRX19013691 |
| SRA |
SRX19013690 |
| SRA |
SRX19013688 |
| SRA |
SRX19013687 |
| SRA |
SRX19013686 |
| SRA |
SRX19013685 |
| SRA |
SRX19034726 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7024434_methylation_calls.HepG2.raw.cpg.mfreq.txt.gz |
108.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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