|
| Status |
Public on Nov 23, 2017 |
| Title |
Input exp2 |
| Sample type |
SRA |
| |
|
| Source name |
Cervical carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: Human cervical carcinoma
chip antibody: none
|
| Treatment protocol |
Cells grown to ~90% confluent were fixed directly with 1% formaldehyde.
|
| Growth protocol |
Human cervical carcinoma HeLa cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (v/v) fetal bovine serum (FBS) and antibiotics.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, fixation was stopped by adding Glycine (125mM) and incubating for 5 min at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300–500 bp average in size through sonication. Resultant was immunoprecipitated with MCM7 antibodies 18 hr at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 3 h. After washing and elution, the protein–DNA complex was reversed by heating at 65°C 6hr. Immunoprecipitated DNA was purified by phenol/chloroform extraction and ethanol precipitation.
According to Illumina protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
PRJDB5845
|
| Data processing |
The sequence reads were aligned to the hg19 genome using the Bowtie software (version 0.12.8; parameter -v3 -m1).
Signal data (bigWig) were generated using bamCoverage command of deepTools (version 2.4.2) with the option: --smoothLength 60 --binSize 1 --extendReads.
Peak calling was performed using MACS2 (version 2.0.10.20131216).
Genome_build: hg19
Supplementary_files_format_and_content: .bw file available on sample record. ChIP-Seq peak list as tab delimited .txt (available on the series record).
|
| |
|
| Submission date |
Nov 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nozomi Sugimoto |
| E-mail(s) |
sugimoto@phar.kyushu-u.ac.jp
|
| Organization name |
Kyushu University
|
| Street address |
3-1-1, Maidashi, Higashiku
|
| City |
Fukuoka |
| ZIP/Postal code |
812-0054 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE107248 |
Genome wide identification of MCM7 binding sites as replication origins |
|
| Relations |
| BioSample |
SAMD00015878 |
| SRA |
DRX087443 |
