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| Status |
Public on Jun 04, 2020 |
| Title |
B6J_nTr20_Tg_4_batch2_forebrain_RNA |
| Sample type |
SRA |
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| Source name |
Forebrain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Forebrain
age: 8 weeks old
genotype: Tg(n-Tr20)
batch: Batch 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
For forebrain samples, forebrains were isolated, and stored in RNAlater and frozen at -20C. Following ribosomal RNA depletion, the remaining RNA was purified, fragmented, and libraries were prepared using TruSeq Stranded Total RNA with RiboZero-Mouse (Illumina). mRNA libraries for the assessment of translational efficiency in the B6JN and B6JN-nTr20-/- hippocampus were prepared using the TruSeq v2 mRNA kit (Illumina). mRNA was purified using biotin-tagged polydT oligonucleotides and streptavidin-coated magnetic beads. Ribosome profiling libraries were generated from B6N and B6N-nTr20-/- hippocampi. Libraries were constructed as previously described (Ingolia et al., 2012)
RNA libraries were prepared for sequencing using standard Illumina protocols and ribosome profiling libraries were prepared following the protocol described in Ingolia et al., 2012
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
rRNA depleted total RNA
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| Data processing |
Forebrain RNA-seq was quantified using kallisto version 0.42.4 and psuedo-aligned to the Gencode vM20 transcript reference.
Hippocampus RNA-seq was mapped to the mm10 genome with a Gencode vM20 transcript annotation using hisat2 version 2.1.0.
Hippocampus ribosome profiling data were adaptor trimmed with fastx_clipper using -a CTGTAGGCACCATCAAT and rRNA was removed using bowtie2 version 2.2.3 using the parameter -L 13.
Remaining ribosome profiling reads were mapped to the mm10 genome with a Gencode vM20 transcript annotation using hisat2 version 2.1.0.
Hippocampus RNA-seq and ribosome profiling reads were counted at the gene-level using featureCounts. The RNA-seq data was quantifified by counting reads overlapping exons and the ribosome profiling data was quantified by counting reads overlapping CDS regions.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include kallisto estimated counts and TPM values for each forebrain RNA-seq sample at the transcript level.
Supplementary_files_format_and_content: tab-delimited text files include featureCounts estimated gene counts for hippocampus RNA-seq and ribosome profiling samples.
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| Submission date |
Jun 03, 2020 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Scott Adamson |
| E-mail(s) |
scott.adamson@jax.org
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| Organization name |
The Jackson Laboratory
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| Lab |
Chuang
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| Street address |
10 Discovery Drive
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| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE151742 |
Expression of the neuronal tRNA n-Tr20 regulates synaptic transmission and seizure susceptibility |
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| Relations |
| BioSample |
SAMN15096363 |
| SRA |
SRX8465986 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4589673_B6J_nTr20_Tg_4_batch2_forebrain_RNA_abundance.tsv.gz |
4.6 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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