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| Status |
Public on Dec 14, 2016 |
| Title |
pUC19 |
| Sample type |
SRA |
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| Source name |
Human embryonic kidney cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: Human embryonic kidney cell line
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| Treatment protocol |
Unless stated elsewhere, cells were transfected with gRNAs (total 500 ng) and a CRISPRme expression vector (500 ng) in six-well plates using X-tremeGENE 9 DNA transfection reagent (Roche). For single gRNA or pUC19 control transfections, the amount of plasmid added was equivalent to the total amount of plasmid added for multiple gRNA transfections.
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| Growth protocol |
Human embryonic kidney HEK293T cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Life Technologies), 10% fetal bovine serum (Sigma), 1% penicillin-streptomycin (Sigma), 1X GlutaMAX (Life Technologies).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, 69506) according to the manufacturer’s instructions, and subject to WGBS SOP analysis in BGI tech.
For Bisulfite-Seq, genomic DNA was fragmented by sonication to a mean size of 250bp using a Bioruptor (Diagenode, Belgium). Bisulphite conversion was conducted with the EZ DNA Methylation-Gold kit (ZYMO). The libraries were sequenced on Illumina HiSeq X Ten. The 48502 bp lambda DNA was used as an extra reference for calculating the bisulphite conversion rate. Nearly complete (>99%) bisulfite conversion was documented in all libraries.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Description |
g9
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Bisulfite-Seq clean reads were aligned to the human reference genome (hg19) by BSMAP(v2.74) with the parameter “-u -v 5 -z 33 -p 6 -n 0 -w 20 -s 16 -r 0 -f 10 -L 140”.
Only the CpG sites with read depths >=4 were taken into consideration for DNA methylation level calculation.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The cout.gz file for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, coordinate, strand, cytosine type, cytosine context, methylated cytosines reads and unmethylated cytosines reads.
Supplementary_files_format_and_content: The bedGraph format files for each cytosine context with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (%) (#methylated cytosines reads/#total cytosines reads).
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| Submission date |
Dec 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yonglun Luo |
| E-mail(s) |
alun@biomed.au.dk
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| Phone |
0045-22411944
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| Organization name |
Aarhus University
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| Street address |
Wilhelm Meyers Allé 4
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| City |
aarhus |
| ZIP/Postal code |
8000 |
| Country |
Denmark |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE92310 |
Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA Methylation by dCas9 methyltransferases (CRISPRme) [WGBS] |
| GSE92311 |
Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA Methylation by dCas9 methyltransferases (CRISPRme) |
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| Relations |
| BioSample |
SAMN06134715 |
| SRA |
SRX2417154 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2425586_g9.bedGraph.gz |
3.2 Gb |
(ftp)(http) |
BEDGRAPH |
| GSM2425586_g9.cout.txt.gz |
3.2 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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