|
| Status |
Public on May 19, 2021 |
| Title |
TE5_TP63_KD_Input |
| Sample type |
SRA |
| |
|
| Source name |
TE5_TP63_KD_Input
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: esophageal squamous cell carcinoma
genotype: TP63_KD
|
| Growth protocol |
TE5 is maintained in Dulbecco’s modified Eagle medium (DMEM). The medium is supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Paired end 151 bp reads were aligned to the hg19 reference genome using Bowtie2.
PCR duplicate reads were removed using Picard MarkDuplicates.
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads
|
| |
|
| Submission date |
Apr 20, 2020 |
| Last update date |
May 19, 2021 |
| Contact name |
Pushkar Dakle |
| Organization name |
Cancer Science Institute of Singapore
|
| Street address |
14 Medical Dr
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE148920 |
Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma |
|
| Relations |
| BioSample |
SAMN14643856 |
| SRA |
SRX8142109 |
