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| Status |
Public on Aug 22, 2017 |
| Title |
Negative WGBS |
| Sample type |
SRA |
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| Source name |
HEK 293T
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK 293T
cell type: Human epithelial HEK 293T cells
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| Treatment protocol |
HEK293T cells were infected by dCas9-SunTag-DNMT3A for 30 days. We purified fluoscent-positive cells and performed RNA-seq.
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| Growth protocol |
ATCC-formulated Dulbecco's Modified Eagle's Medium and 10% fetal bovine serum
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction by Purelink extraction kit
bisulfite treated DNA was made into library with Illumina TruSeq DNA sample preparation kit
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
library strategy: WGBS
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| Data processing |
use BSMAP-2.90 to align bisulfite-treated sequencing reads to the human genome hg19 of bisulfite treated data
use moabs to compute the methylation ratio of single base level
Genome_build: hg19
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context, methylation ratio, number of effective total C+T counts on this locus, number of total C counts on this locus, number of total C+T counts on this locus, number of total G counts on this locus of reverse strand, number of total G+A counts on this locus of reverse strand, lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval
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| Submission date |
Apr 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jianzhong Su |
| E-mail(s) |
[email protected]
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| Phone |
8322902241
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| Organization name |
Baylor college of Medicine
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| Street address |
1 Baylor Plaza
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| City |
HOUSTON |
| State/province |
TEXAS |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE97814 |
DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [WGBS] |
| GSE97816 |
DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A |
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| Relations |
| BioSample |
SAMN06758257 |
| SRA |
SRX2737702 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2578866_Neg_WGBS_CG.txt.gz |
133.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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