|
| Status |
Public on Feb 24, 2021 |
| Title |
m12-MBD-ChIP |
| Sample type |
SRA |
| |
|
| Source name |
human mesothelioma cell line m12
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: m12
tissue: human mesothelioma cell line
|
| Growth protocol |
Human mesothelioma cell lines were maintained in RPMI with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with formadihyde, sonicated to 100-1000bp, and immunoprecipitated with active motif MBD2b/MBD3L1 recombinant proteins.
Illumina DNA library was prepared with NEB DNA ultra II kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
fastq files was generated at the basespace cloud
fastq files was aligned to human genome using Bowtiew to generate bam files
MACS2 Peak calling
fetches nearest gene around the peaks
annotate genes
Genome_build: GRCh37
Supplementary_files_format_and_content: MACS2-called-peaks
Supplementary_files_format_and_content: nearest-genes-of-peaks
Supplementary_files_format_and_content: unique-gene-symbols
|
| |
|
| Submission date |
Sep 29, 2020 |
| Last update date |
Feb 24, 2021 |
| Contact name |
yinfei tan |
| E-mail(s) |
Yinfei.Tan@fccc.edu
|
| Phone |
2157282898
|
| Organization name |
Fox Chase Cancer Center
|
| Department |
Genomic Core
|
| Lab |
NGS-research
|
| Street address |
333 cottman ave
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19111 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE158768 |
RIPK3 is a tumor suppressor in mesothelioma |
|
| Relations |
| BioSample |
SAMN16293902 |
| SRA |
SRX9216304 |
