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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 10, 2015 |
| Title |
WT_AL_ZT06_A_RNA |
| Sample type |
SRA |
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| Source name |
Liver Total RNA
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
age: 10-14 weeks
feeding: Ad Libitum
genotype: Wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Liver RNAs were extracted as previously described (Gachon et al, 2006) with classical methods using guanidium thiocyanate lysis buffer.
Libraries were prepared using the TruSeq Stranded Total RNA Sample Prep Kit with the Ribo-Zero Gold depletion set (Illumina) following the manufacturer’s protocol. We used 250 ng total RNA as starting material and performed 11 PCR cycles from library amplification (optimal cycle determined with the same method as the small RNA, see above). Samples were pooled by 24, denatured, spiked with 3% PhiX and loaded onto a paired-end read flow cell v3 at a final concentration of 11 pM for a paired-end 100 cycles run, strictly following Illumina’s recommendations. Sequencing depth was equivalent to 3 samples per lane.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Paired end reads were aligned to the genome index build with Ensembl annotation index using STAR with option --alignIntronMax 1000000
Using Ensembl annotations, we defined a gene body by merging all the respective transcripts using Bedtools(70). A region is defined as exonic if it occurs in a least one of the transcripts while an intronic region has to be shared between all the transcripts. Using a custom Perl script, we assigned uniquely mapping paired-reads to exonic region (exon/exon and complete exon reads) or intronic region (intron-exon and complete intron reads) considering reads orientation
Reads count were normalized by the total library size and size of the sum of the respective intronic or exonic region. Log2 expression levels were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Log2 Normalized read count (RPKM)
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| Submission date |
Sep 29, 2015 |
| Last update date |
Jul 06, 2021 |
| Contact name |
Frédéric Gachon |
| E-mail(s) |
[email protected]
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| Phone |
+41 791926057
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| Organization name |
University Of Queensland
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| Department |
Institute for Molecular Bioscience
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| Street address |
306 Carmody Road
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| City |
St Lucia |
| State/province |
QLD |
| ZIP/Postal code |
4072 |
| Country |
Australia |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE73552 |
Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver [RNASeq] |
| GSE73554 |
Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver |
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| Relations |
| BioSample |
SAMN04122069 |
| SRA |
SRX1295075 |
| 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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