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| Status |
Public on Jun 11, 2024 |
| Title |
dhh1Δ, rep1 |
| Sample type |
SRA |
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| Source name |
dhh1{delta}
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell line: dhh1{delta}
genotype: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}1 dhh1{delta}
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
2 ml mid-log-phase cells were collected by centrifugation and resuspended in 400 µl TE solution. Add 400 µl acid phenol (CHCl3) to the cells and vortexed vigorously for 10 s. Incubate for 60 min at 65°C, vortexing every 15 min. Then, place on ice for 5 min and spin at 16,000 × g for 10 min at 4°C. Transfer the supernatant to a new tube , add 400 µl CHCl3 and vortex vigorously for 10 s, and then spin at 16,000 × g for 10 min at 4°C. Transfer the supernatant to a new tube, add a 1/10 volume of 3 M NaAc, pH 5.2, and 2.5 volumes EtOH. Put the tube at -80°C for 60 min and centrifugate at 16,000 × g for 10 min at 4°C. Wash the pellet twice with 80% EtOH and dry by air. DNase I treatment was performed at 37°C to remove potential gDNA contamination.
cDNA were synthesized by ProtoScript® II Reverse Transcriptase with d(T)23VN primer according to the manufacturer’s manual. Synthesized cDNA hybrids were sonicated to 250 bp using ME220 (Covaris, 70 W, 20% Duty factor, 1000 cycles per burst, 130 s, at 4 – 20°C). Denaturation was performed by heating at 95°C for 2 minutes followed by immediately cooling on ice for 2 minutes. Then,the tailing and single-strand ligation method was used for library preparation used as mDRIP-seq Input library construction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
dhh1Δ-R1
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| Data processing |
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Raw reads with low quality and adaptor contamination were trimmed, and short reads less than 50 pb were filtered by Trim Galore (version 0.6.7)
After trimmingl, clean reads were aligned to the sacCer3 genome by using Bowtie 2 (version 2.2.5) with default parameters.
Raw counts for the feature of genes were extracted by featureCounts (version 2.0.3).
Assembly: sacCer3
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
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| Submission date |
Oct 27, 2023 |
| Last update date |
Jun 11, 2024 |
| Contact name |
Changbin Sun |
| Organization name |
Chinese Academy of Agricultural Sciences
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| Department |
Agricultural Genomics Institute at Shenzhen
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| Lab |
Guangdong Laboratory of Lingnan Modern Agriculture
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| Street address |
Dapeng
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| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
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| Platform ID |
GPL27812 |
| Series (2) |
| GSE219071 |
mDRIP-seq is a high-throughput method for quantitative R-loop landscape profiling |
| GSE246423 |
mDRIP-seq: a high-throughput method for R-loop mapping and quantitative assessment. |
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| Relations |
| BioSample |
SAMN38019630 |
| SRA |
SRX22250525 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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