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| Status |
Public on Apr 30, 2019 |
| Title |
mouse_0_2 |
| Sample type |
SRA |
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| Source name |
embryonic fibroblasts
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| Organism |
Mus musculus |
| Characteristics |
rhps4 treatment: 0um
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| Treatment protocol |
Mouse embryonic fibroblasts (MEFs), C2C12 myoblasts and HeLa cells were grown in DMEM medium supplemented with 25 mM glucose, 4 mM glutamine, 110 mg/ml pyruvate, 10% (v/v) FBS:FCS (1:1), 100 U/ml penicillin and 100 mg/ml streptomycin at 37°C under standard conditions (5% CO2; ambient O2; 95% relative humidity). HeLa cells were verified by SNP genotyping at the University of Pittsburgh HSCRF Genomics Research Core. Subconfluent wild type MEFs and HeLa cells were cultivated in media containing RHPS4 at indicated concentration (0, 1, 2, or 10 µM) and time (16 or 24h). Drug wash-out was performed by pre-warmed media replacement. EtBr treatment was conducted on subconfluent MEFs for 24 h in the presence of 25 or 250 ng/ml compound. Cells were collected by trypsinization, pelleted at 200 RCF for 5 min, washed with PBS, and flash freezed in liquid nitrogen for later DNA or RNA preparation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA concentration and quality from each sample was assessed using Qubit 2.0 fluorometer (ThermoFisher Scientific) and Agilent TapeStation 2200 (Agilent, Santa Clara, CA)
Total RNA libraries were generated using Illumina TruSeq Stranded Total RNA Sample Preparation Guide Rev. E (Illumina, San Diego, CA). In brief, this process depletes nuclear ribosomal RNA (rRNA) and then fragments the remaining RNA, which was converted into first strand cDNA using reverse transcriptase and random primers. The second strand cDNA is generated using DNA polymerase I and RNase H. The cDNA fragments were further processed for adapter ligation, and then enriched with PCR to create the final cDNA library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Quality control for raw fastq files were performed with FastQC
Low quality reads and 3’ adapters were trimmed with Trim Galore! and Cutadapt.
The trimmed reads were aligned to mm10 with the RNA-seq aligner STAR v2.5.2a
Gene expressions of every sample were quantified by counting the number of unique fragments mapped to genes using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts of genes for each sample.
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| Submission date |
Aug 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ting Wang |
| E-mail(s) |
wang9ting@gmail.com
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| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
Clinical Research
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| Street address |
1100 Fairview Ave. N.
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE103116 |
Implication of G-quadruplexes in mitochondrial gene expression and genome replication |
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| Relations |
| BioSample |
SAMN07560529 |
| SRA |
SRX3134821 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2753976_mouse_0_2.txt.gz |
128.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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