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| Status |
Public on Jan 18, 2023 |
| Title |
DPY30mAID_24h_TT_seq_Rep2 |
| Sample type |
SRA |
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| Source name |
mESCs
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| Organism |
Mus musculus |
| Characteristics |
cell type: mESCs
strain: 129/Ola
genotype: DPY30mAID
time poin: 24h
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| Treatment protocol |
For DRB/TTchem-seq, cells were incubated in 100 µM DRB (Sigma-Aldrich, D1916) for 3.5 h. The cells were then washed twice in PBS, and the pre-warmed fresh DRB-free medium was added to restart transcription. The RNA was labeled in vivo with 1 mM 4sU for 10 min before the addition of QIAzol, which was used to stop the reaction at the desired time point.
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| Growth protocol |
E14 ESCs (129/Ola background) were maintained on 0.2% gelatin-coated plates in Glasgow Minimum Essential Medium (GMEM, Sigma-Aldrich, G5154) containing 15% fetal bovine serum (Gibco, 26140079), supplemented with 1× Pen-Strep (Thermofisher Scientific, 15140122), 2 mM Glutamax (Thermofisher Scientific, 35050061), 50 µM β-mercaptoethanol (Thermofisher Scientific, 21985023), 0.1 mM nonessential amino acids (Thermofisher Scientific, 11140050), 1 mM sodium pyruvate (Thermofisher Scientific, 11360070), and Leukemia Inhibitory Factor (LIF, 1000U/mL, Millipore).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Following the specified treatment, we supplemented the treatment medium with 1 mM 4-thiouridine (4sU) and metabolically labeled the cells for 10 min. The cells were lysed in QIAzol (Qiagen, 79306) and total RNA was isolated according to the manufacturer’s instructions before the addition of 100 ng RNA spike-in mix together with QIAzol.
Libraries were constructed using TruSeq Stranded Total RNA kit (Illumina, 20020596).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Data processing |
Library strategy: TT-seq
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
Paired-end reads were demultiplexed by bcl2fastq. Raw reads were aligned to the mouse mm10 genome assembly using STAR.
Further data processing was carried out using the R/Bioconductor environment.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
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| Submission date |
Aug 09, 2021 |
| Last update date |
Jan 18, 2023 |
| Contact name |
Hua Wang |
| E-mail(s) |
moodswh@gmail.com
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| Organization name |
Memorial Sloan Kettering Cancer Center
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| Street address |
430 East 67th Street
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL21626 |
| Series (2) |
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| Relations |
| BioSample |
SAMN20671040 |
| SRA |
SRX11678511 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5509826_DPY30mAID_24h_TT_seq_Rep2.bw |
43.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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