|
| Status |
Public on Sep 29, 2021 |
| Title |
RNA-seq_DMSO_SPT5-fkbp-DLD1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SPT5-DMSO DLD1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colorectal adenocarcinoma cell lines
treatment: untreated
|
| Treatment protocol |
Cells were treated with DMSO or dTAG-13 for 12h, or 24h.
|
| 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 |
total RNA |
| Extraction protocol |
RNA was isolated with TRIzol.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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 and mouse mm10 assemblies using STAR v2.7.5c with parameter "--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 2 --outSJfilterReads Unique"
PCR duplicates were removed using Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The number of spike-in mm10 reads was counted with SAMtools v1.9 and normalization factor alpha = 1e6/mm10_count was calculated (Li et al., 2009).
Strand-specific RNA-seq signal normalized by spike-in reads was generated by deeptools v3.5.0 (Ramirez et al., 2016).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files
|
| |
|
| 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) |
| GSE180843 |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [RNA-seq] |
| GSE180845 |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 |
|
| Relations |
| BioSample |
SAMN20407866 |
| SRA |
SRX11555407 |
