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| Status |
Public on May 17, 2022 |
| Title |
Liver_WT_CT14_rep1 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain: C57BL/6
genotype: WT
time: CT14
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mouse livers from the mutant and WT male mice harvested at six time points throughout the day (CT2, 6, 10, 14, 18, and 22; n=2) were placed in Lysing Matrix D tubes (MP Biomedicals) with TRIzol reagent (Invitrogen), and homogenized by using Fast-Prep 24 instrument (MP Biomedicals). Total RNAs were prepared with the RNeasy Mini Kit (Qiagen), followed by ethanol precipitation. Poly(A)-tailed RNA was isolated from the total RNA by using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, #E7760).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
WT_CT14_1
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| Data processing |
Illumina RTA3.4.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and quality-controlled using trimmomatic v0.39, then mapped to mm10 whole genome using HISAT2 v2.1.0 with parameters -p 8 -q -x mm10
Fragments Per Kilobase of exon per Million mapped reads (FPKM) were calculated using StringTie v1.3.5 - Ballgown v2.18.0 pipeline. Transcripts annotation file was obtained from Ensembl95.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample
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| Submission date |
Mar 21, 2022 |
| Last update date |
May 18, 2022 |
| Contact name |
Satoshi Kawakami |
| E-mail(s) |
[email protected]
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| Organization name |
The University of Tokyo
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| Department |
The Institute of Medical Science
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| Street address |
4-6-1 Shirokanedai
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| City |
Minato City |
| ZIP/Postal code |
108-8639 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE199061 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and delta-RRE Liver Transcriptomes |
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| Relations |
| BioSample |
SAMN26849536 |
| SRA |
SRX14530700 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5963463_WT_CT14_1.txt.gz |
431.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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