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Sample GSM2425586 Query DataSets for GSM2425586
Status Public on Dec 14, 2016
Title pUC19
Sample type SRA
Source name Human embryonic kidney cells
Organism Homo sapiens
Characteristics cell line: HEK293T
cell type: Human embryonic kidney cell line
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.
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).
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.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
Description g9
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).
Submission date Dec 13, 2016
Last update date May 15, 2019
Contact name Yonglun Luo
Phone 0045-22411944
Organization name Aarhus University
Street address Wilhelm Meyers Allé 4
City aarhus
ZIP/Postal code 8000
Country Denmark
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)
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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