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| Status |
Public on Feb 25, 2015 |
| Title |
rpn_BIC12h_rep1 |
| Sample type |
SRA |
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| Source name |
Primary hippocampal neuron culture
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
developmental stage: DIV 28
treatment protocol: bicuculline (Tocris, 40 μM), treated for 12h
growth protocol: Dissociated hippocampal neurons prepared as in Aakalu, G., et al., Dynamic visualization of local protein synthesis in hippocampal neurons. Neuron, 2001. 30(2): p. 489-502.
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| Extracted molecule |
total RNA |
| Extraction protocol |
TRIZOL (Invitrogen) extraction
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 HiSeq 2500 |
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| Description |
Sample 23
rRNA depleted
rat_TPM.txt, rat_circRNA_TPM.txt
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| Data processing |
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 or rn5.0 whole genome using Tophat2 v2.0.6 with parameters -N 6 --read-edit-dist 6 --segment-mismatches ---transcriptome-index=index, where the transcriptome-index is build on Ensembl annotation verion 67 for mouse and version 72 for rat
Fragments Per Kilobase of gene transcripts per million mapped reads (FPKM) were calculated using Cufflinks version 2.2.1 with parameter -u. Then FPKMs were converted to TPM following the protocol from Bo Li et at., BMC Bioinformatics, 2009
CircRNAs are identified and then quantified using the acfs pipeline available at https://code.google.com/p/acfs/
Genome_build: mm9 and rn5.0
Supplementary_files_format_and_content: tab-delimited text files include TPM values for TTO and circRNAs in mouse and rat samples
Supplementary_files_format_and_content: bed files for circRNAs in mouse and rat
Supplementary_files_format_and_content: mouse_TPM.txt: abundance measurements for mRNAs and lincRNAs
Supplementary_files_format_and_content: mouse_circRNA_TPM.txt: abundance measurements for circRNAs
Supplementary_files_format_and_content: mouse_circRNA_MEA.bed: bed file for highly-confident circRNAs
Supplementary_files_format_and_content: mouse_circRNA_CBR.bed: bed file for less-confident circRNAs
Supplementary_files_format_and_content: rat_TPM.txt: abundance measurements for mRNAs and lincRNAs
Supplementary_files_format_and_content: rat_circRNA_TPM.txt: abundance measurements for circRNAs
Supplementary_files_format_and_content: rat_circRNA_MEA.bed: bed file for highly-confident circRNAs
Supplementary_files_format_and_content: rat_circRNA_CBR.bed: bed file for less-confident circRNAs
Supplementary_files_format_and_content: PacBio_CCS.fa: Only the Circular Consensus (CCS) Reads were used to support the circular structure and the full-length sequence of the circRNAs
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| Submission date |
Jan 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xintian Arthur YOU |
| Organization name |
Max-Delbrueck-Center for Molecular Medicine
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| Street address |
Robert-Roessle-str. 10
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| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE61991 |
Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity |
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| Relations |
| BioSample |
SAMN03294589 |
| SRA |
SRX852598 |
| 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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