|
| Status |
Public on May 04, 2018 |
| Title |
(II) N2A__rRNA_dep__Sfpq_KD |
| Sample type |
SRA |
| |
|
| Source name |
Neuro-2a
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6+C57BL/6J+CBA
cell type: Neuro-2a
treatment: siRNA for mSfpq, using RNAiMAX
growth condition: differentiated condition
rna type: polyA(+/-) RNA
|
| Treatment protocol |
Knockdown of Sfpq was conducted with reveres transfection using Stealth siRNA and RNAiMAX in differentiation media of D-MEM with 2% FCS, glutamine, and antibiotics (Penicillin/Streptomycin).
|
| Growth protocol |
Neuro-2A cell was expanded in D-MEM with 10% FCS, glutamine, and antibiotics (Penicillin/Streptomycin) .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according to Life Techonology's instructions accompanying the Ion AB Library Builder™ System and Library Builder. Briefly, total RNA was treated with RiboMinus™ Eukaryote System v2 (Life technologies, Carlsbad, CA, USA) to ribosomal RNA-depleted RNA. RNA libraries were then prepared using the Life Techonology Ion Total RNA-Seq Kit for the AB Library Builder™ System and Library Builder. High-throughput sequencing was performed using the Ion Proton System. Sfpq mRNA level was down-regulated less than 10% in Neuro-2a treated with Sfpq-siRNA comparing those of Luc-siRNA.
Total RNA from Neuro-2a cells were extracted using RneasyMidi (Qiagen) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
RNA-seq (polyA+/-) data for Sfpq-knockdown Neuro-2a cells
|
| Data processing |
Basecalls performed using Torrent Suite version 4.0.2
Reads which lengths were >= 50 and average sequencing quality scores were >= 17, were used for the study.
Reads mapped to rRNA or tRNA sequences were removed from the following analysis.
The seuqence data was mapped to the genome sequence with Tophat ver. 2.0.10.
Genome_build: mm9
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with an in-house perl script. We counted read counts mapped on exons, then normalized them with library sizes and sum of exon lengths (RPKM; Reads Per Kilobase of exon Model per million mapped reads). In the processed data files, gene ID and RPKM values were described column 1 and 2, respectively.
|
| |
|
| Submission date |
Aug 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kei IIDA |
| E-mail(s) |
kiida@life.kindai.ac.jp
|
| Organization name |
Kindai University
|
| Street address |
Kowakae 3-4-1
|
| City |
Higashi-Osaka |
| State/province |
Osaka |
| ZIP/Postal code |
5778502 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18635 |
| Series (2) |
| GSE60241 |
The RNA-binding protein Sfpq regulates long neuronal genes in transcriptional elongation [Neuro2A cells] |
| GSE60246 |
The RNA-binding protein Sfpq regulates long neuronal genes in transcriptional elongation |
|
| Relations |
| BioSample |
SAMN02979115 |
| SRA |
SRX5604079 |
