|
| Status |
Public on Sep 29, 2021 |
| Title |
PRO_dTAG-3h_SPT5-dTAG_DLD1_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SPT5-dTAG DLD1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD1
cell type: colorectal adenocarcinoma cells
treatment: treated with dTAG13 for 3 hours
genotype: SPT5 knock-in of a dTAG tag
|
| Treatment protocol |
Cells were treated with DMSO or dTAG 13 for 3h.
|
| 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.
Enriched RNA was ligated with RNA adapters. Reverse transcription (RT) was performed using the Superscript III enzyme (Invitrogen). The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix. Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Library strategy: PRO-Seq
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 --length 15” .
Ribosomal RNA reads were removed using Bowtie v2.3.5.1 with “--un-conc-gz” (Langmead and Salzberg, 2012)
The remaining reads were aligned to hg19 or mm10 genome using Bowtie v2.3.5.1 with “--local --sensitive-local” (Langmead and Salzberg, 2012).
Removal of low mapping quality reads and duplicated reads and calculation of normalization factor were performed with SAMtools v1.9 (Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
Strand-specific PRO-seq signal normalized by spike-in reads was generated by deeptools v3.5.0 (Ramirez et al., 2016) with "--Offset 1" for single-base files and "--Offset None" for full-length files.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Sep 06, 2021 |
| Last update date |
Sep 29, 2021 |
| Contact name |
Linna Peng |
| E-mail(s) |
[email protected]
|
| Phone |
8618810567356
|
| Organization name |
Fudan University
|
| Street address |
Dong'an Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE180845 |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 |
| GSE183505 |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [PRO-seq] |
|
| Relations |
| BioSample |
SAMN21242924 |
| SRA |
SRX12024432 |
