|
| Status |
Public on Aug 31, 2024 |
| Title |
Interphase HeLa, GFP, control, CUT&Tag (C1) |
| Sample type |
SRA |
| |
|
| Source name |
Stably expressing GFP HeLa cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Stably expressing GFP HeLa cell
|
| Treatment protocol |
thymidine 2mM 16 h to block the cell in G1/S (interphase)；Nocodazole 100 ng/ml 16 h to block the cell in G2/M (mitosis)
|
| Growth protocol |
HeLa cells were maintained in DMEM (Gibco) with 10% fetal bovine serum (HyClone) and 100 units/ml penicillin (Gibco) plus 100 μg/ml streptomycin (Gibco)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
See Vazyme TD904
Next-generation sequencing library preparations were constructed following the manufacturer’s protocol (Vazyme TD202)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Illumina NovaSeq PE150
HeLa-C1-GFP
|
| Data processing |
*library strategy: CUT&Tag
Then libraries with different indices were multiplexed and loaded on an Illumina Novaseq instrument according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150 paired-end (PE) configuration, and image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument. In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt to be high-quality clean data. The clean data then are aligned to the reference genome via software Bowtie2. Use MACS to analyze peaks quality control, peaks calling and peaks annotation. To find the common and unique peaks of several groups, HOMER(V2) toolkit is used to treat the peaks with 200bp overlapping peaks as common and vice versa.
Assembly: GRCh38.109
Supplementary files format and content: The processed data consisted of a bw file for each sample and a table of the corresponding peaks
|
| |
|
| Submission date |
Aug 01, 2024 |
| Last update date |
Aug 31, 2024 |
| Contact name |
张 婷 |
| E-mail(s) |
jocelynz@mail.ustc.edu.cn
|
| Phone |
18895364168
|
| Organization name |
中国科学技术大学
|
| Street address |
安徽省合肥市蜀山区黄山路443号中国科学技术大学西校区生命科学学院547室
|
| City |
hefei |
| State/province |
Select an option… |
| ZIP/Postal code |
230027 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE273759 |
Dynamic phosphorylation of FOXA1 by Aurora B guides post-mitotic gene reactivation |
|
| Relations |
| BioSample |
SAMN42993284 |
| SRA |
SRX25571235 |
