|
| Status |
Public on Sep 23, 2013 |
| Title |
Western Blot samples HB-5 3 HBB102 |
| Sample type |
SRA |
| |
|
| Source name |
K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562 cells
target loci: Western Blot samples HB-5 3
|
| Treatment protocol |
Cells were transfected (by nucleofection or lipofectamine) with plasmids encoding TALE-TET1 fusions
|
| Growth protocol |
K562, HeLa and 293 cells were grown under standard growth conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using the Qiagen Blood Mini kit and bisulfite treated. Bisulfite converted genomic DNA was PCR amplified with locus-specific primers.
Libraries were prepared using standard illumina multiplex library prep protocols. Adapters were added either by PCR or by ligation
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
032813_MM397_analysis.csv
|
| Data processing |
sequence reads were mapped using BSMAP v2.74 with default parameters
CPG counts determined by BSMAP were summarized and output to Excel files
Genome_build: hg19 or RHOXF2 reference sequence
Supplementary_files_format_and_content: processed data files are csv files summarizing the total number of methylated and unmethylated Cs in each sample
|
| |
|
| Submission date |
Sep 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Morgan Lee Maeder |
| E-mail(s) |
morganlmaeder@gmail.com
|
| Organization name |
Mass General Hospital
|
| Street address |
149 13th St
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE50761 |
Targeted DNA demethylation using TALE-TET1 fusion proteins |
|
| Relations |
| BioSample |
SAMN02353510 |
| SRA |
SRX348295 |
