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Sample GSM1468510 Query DataSets for GSM1468510
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

Supplementary file Size Download File type/resource
GSM1468510_N2A_mRNA_seq_Sfpq_KD.rep2.rpkm.txt.gz 201.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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