|
| Status |
Public on Jun 07, 2022 |
| Title |
anti_FoxM1_chip_2_ACGAGAAC-ACAGTTCG_L003_R1_001.fastq.gz |
| Sample type |
SRA |
| |
|
| Source name |
Huh7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Huh7
cell type: HCC Cell line
treatment: No treatment
antibody: Anti-FOXM1 Antibody (G-5): sc-376471
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Human HCC Huh7 cells were obtained from American Type Culture Collection. All experiments were performed within 8 to 10 passages. Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (HyClone Laboratories Inc.), with 100 units of penicillin/streptomycin used to culture cells at 37ºC with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIPseq libraries were prepared with the Hyper Library Construction Kit from Kapa Biosystems with two modifications: adaptors were diluted 1:20 and adaptored DNA were amplified for 10 cycles.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the GRCH38 genome assembly using BWA
Data were filtered using the SAM tools and bed graph were generated
peaks were called using MACS2 version 2.2.7.1 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5).
Genome_build: GRCH38
Supplementary_files_format_and_content: BigWig files were generated using WigToBigWig
|
| |
|
| Submission date |
Jun 08, 2021 |
| Last update date |
Jun 07, 2022 |
| Contact name |
Vaibhav Chand |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Illinois at Chicago
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
Pradip Raychaudhuri's Lab
|
| Street address |
900S Ashland Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60607 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE176383 |
Global enrichment of FoxM1 bound chromatin in Huh7 cell line |
|
| Relations |
| BioSample |
SAMN19606828 |
| SRA |
SRX11094198 |
