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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 27, 2021 |
| Title |
Sirt1KO-1 |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
background strain: 129Sv/J
gender: Male
cell type: embryonic stem cells
genotype: Sirt1 KO
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA isolated using Qiagen RNeasy mini kit.
The integrity of the total RNA was determined using a bioanalyzer (Agilent) and concentration were assessed by Qubit (ThermoFisher Scientific). A TruSeq RNA kit (Illumina, San Diego, CA) was utilized to prepare the poly(A)-enriched RNA-seq libraries that were sequenced on the Illumina NovaSeq 6000 in a 75-base paired-end mode according to the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
RNA-SEQ reads (223-283M per sample) were aligned to the UCSC mm10 reference genome using STAR
The quantification results from FeatureCounts were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Genome_build: mm10
Supplementary_files_format_and_content: excel table; log2 transformed and normalized abundance measurements by DESeq2
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| Submission date |
Dec 28, 2020 |
| Last update date |
May 27, 2021 |
| Contact name |
Xiaojiang Xu |
| Phone |
984-287-3622
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| Organization name |
NIEHS
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| Lab |
ESCBL
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| Street address |
111 T. W. Alexander Dr.,
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| City |
RTP |
| State/province |
North Carolina |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE163920 |
The role of SIRT1 in regulation of transcription and splicing in mouse embryonic stem cells |
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| Relations |
| BioSample |
SAMN17170470 |
| SRA |
SRX9741023 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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