|
| Status |
Public on Sep 29, 2021 |
| Title |
TT-seq_dTAG-3h_SPT5-dTAG-DLD1_rep2 |
| 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. Add 4SU directly to the tissue culture medium to a final concentration of 500 μm. Incubate the cells with 4SU for 15 min.
|
| 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 NovaSeq 6000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Library strategy: TT-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” .
The remaining reads were aligned to human hg19 and mouse mm10 assemblies using STAR v2.7.5c with parameters “-outFilterMultimapNmax 1 -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.02 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate” (Dobin et al., 2013).
SAMtools v1.9 (Li et al., 2009) was used to quality filter SAM files with “-q 7 -f 2” and duplicated reads were removed using Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The counts of spike-in mm10 reads were used to generate normalization factors for coverage profiles.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files
|
| |
|
| 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 |
| GSE183506 |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [TT-seq] |
|
| Relations |
| BioSample |
SAMN21242904 |
| SRA |
SRX12024409 |
