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| Status |
Public on Jul 19, 2021 |
| Title |
3K_PBS_D6_1 |
| Sample type |
SRA |
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| Source name |
Primary cortical neuron cultures
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| Organism |
Rattus norvegicus |
| Characteristics |
aav treatment: AAV-aSyn 3K
days post aav for rna isolation: Day 6
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| Treatment protocol |
Rat cortical neuron cultures were treated with AAV9-EV or AAV9-3K aSyn on DIV 5. RNA was isolated 6-, 12-, and 19-days post AAV treatment
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with a Rneasy plus kit with Dnase I digestion from Qiagen.
Full length cDNA was prepared with the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, 634891) according to manufacturer’s instructions from 8 ng of input RNA.
Libraries were prepared from amplified cDNA using the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096) according to manufacturer’s instructions. 150 pg of cDNA was used as input, 12 cycles of PCR were used to amplify tagmented cDNA with Nextera Index Kit Set A (Illumina, FC-131-2001), and library cleanup was performed as recommended for 300-500bp libraries. Libraries were quantified and QCed on the Lab Chip GX DNA HS Chip (Perkin Elmer, CLS760672). Libraries were normalized to 10 nM, pooled, and sequenced on a HiSeq 2500 in paired end mode 2x50 bp to an average depth of 8.8m reads per sample.
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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 |
RNA-Seq read data was analyzed using a pipeline that used STAR (version 2.5.2b) for read alignment and RSEM (version 1.2.31) transcript read count quantification
All samples passed quality checks on raw reads with FASTQC and read alignment quality (>90% uniquely mapped paired reads).
Counts were normalized by DESeq2 across all samples
Genome_build: Rnor_6.0 (GCA_000001895.4)
Supplementary_files_format_and_content: Matrix table with normalized counts for every gene and every sample
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| Submission date |
Apr 20, 2021 |
| Last update date |
Jul 19, 2021 |
| Contact name |
Justin Nicholatos |
| E-mail(s) |
jwnichol1@gmail.com
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| Organization name |
Biogen
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| Department |
Neurodegeneration
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| Street address |
225 Binney St
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| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE172385 |
Project_Summary_Rat_primary_cortical_neurons_asyn_3K_RNA_Seq |
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| Relations |
| BioSample |
SAMN18806709 |
| SRA |
SRX10641125 |
| 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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