|
| Status |
Public on Sep 29, 2021 |
| Title |
ATAC_Spt5_dTAG_3h_rep1_DLD1 |
| Sample type |
SRA |
| |
|
| Source name |
SPT5-dTAG DLD1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colorectal adenocarcinoma cell lines
treatment: treated with dTAG13 for 3 hours
|
| Treatment protocol |
One replicate was DMSO or dTAG-13 treated for 3 hours.
|
| Growth protocol |
Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated with PCR clear-up.
Libraries were prepared according to Vazyme's instructions accompanying the TruePrep DNA Library Prep Kit V2 (Vazyme TD501-02). Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to human (hg19) genome assembly using Bowtie 2 v2.3.5.1 with parameters “-N 1 -L 25 -X 2000 --no-mixed --no-discordant” (Langmead and Salzberg, 2012).
All unmapped reads, low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9(Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
Reads counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) with deeptools v3.5.0 and peaks were called using macs2 v2.2.6 (Ramirez et al., 2016; Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files include FPKM values for each Sample
|
| |
|
| Submission date |
Jul 26, 2021 |
| Last update date |
Sep 29, 2021 |
| Contact name |
Linna Peng |
| E-mail(s) |
penglinna7@gmail.com
|
| Phone |
8618810567356
|
| Organization name |
Fudan University
|
| Street address |
Dong'an Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE180844 |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [ATAC-seq] |
| GSE180845 |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 |
|
| Relations |
| BioSample |
SAMN20407856 |
| SRA |
SRX11555376 |
