 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 16, 2024 |
| Title |
GA ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
293T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: 293T
|
| Treatment protocol |
1.ATAC-seq was applied to 293T, HeLa, HepG2 and MCF7 cell line. 2.ATAC-seq was applied to mouse liver rhythm model.3. ChIP-seq was applied to different cells with different treatment.
|
| Growth protocol |
Cell lines 293T were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and Pen-Strep (100 U / ml penicillin, 100 mg / ml streptomycin) at 37℃, 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested and wash once with cold 1x PBS buffer, and then resuspended in 1 mL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1mM PMSF). This cell lysis reaction was incubated on ice for 10 min.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina（）.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
In one of my ATAC-seq experiment, 293T cells were crosslinked, permeabilized and incubated with transposons. After tagmentation with transposons, the mixture was incubated with Q Sepharose for 10 min and shortly centrifuged. The supernatant was collected into a new tube as FT (flow-through). The Q Sepharose was then washed with 20 mM, 100 mM, 200 mM, 300 mM, 500 mM, 700 mM, and 1000 mM NaCl successively. The supernatant was collected into new tubes. At last the Q Sepharose was resuspended with 20 mM NaCl as the last group. GA represent the Q Sepharose group. This sample is related to those samples in my last submission (GSE164299)
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 or mm10 whole genome using bowtie2 v2.2.6 with parameters with the parameters -X2000 and -m1.
Remove mitochondrial DNA with removeChrom.py
Peak calling with macs2 v 2.2.1
Motif finding with homer(findMotifsGenome.pl)
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: narrowPeak files were generated using macs2
|
| |
|
| Submission date |
May 18, 2021 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Haizhu Zhang |
| E-mail(s) |
zhz2230@qq.com
|
| Phone |
18621062295
|
| Organization name |
Fudan University
|
| Department |
Institutes of Biomedical Sciences
|
| Lab |
He Fuchu Lab
|
| Street address |
No. 131 Dong'an Road, Xuhui District
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE174642 |
Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon (various cell lines II) |
| GSE174643 |
Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon |
|
| Relations |
| BioSample |
SAMN19243593 |
| SRA |
SRX10921864 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5321302_G50_A_atac.narrowPeak.gz |
1.3 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
