|
| Status |
Public on May 04, 2018 |
| Title |
(I) N2A__mRNA_seq__Sfpq_KD.rep2 |
| 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 Dynabeads® mRNA DIRECT™ Microkit to prepare PolyA-selected messenger 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, replicate 1
|
| 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.
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 |
SAMN02979112 |
| SRA |
SRX5604076 |
