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Sample GSM2936421 Query DataSets for GSM2936421
Status Public on May 05, 2018
Title Sirt6-/- -3
Sample type SRA
 
Source name murine embryonic fibroblast cell
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: murine embryonic fibroblast cell
genotype: Sirt6-/-
Treatment protocol MEF cells were generated from wildtype, Sirt6-/-, P53-/-, or Atm-/-P53-/- mice.
Growth protocol MEF cells were cultured in DMEM (Gibco®) with 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA extracts are first treated with DNase I to degrade DNA contamination. Next, by using the oligo (dT) magnetic beads the mRNA is enriched . Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. The first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with AMPure XP beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using FANSe 2 with parameters -L55 -E4 -I0 -S10 -M0 -U0 -B1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: text files include RPKM values for each Sample
 
Submission date Jan 17, 2018
Last update date May 05, 2018
Contact name Min Xian Qian
E-mail(s) qmx@szu.edu.cn
Organization name Shenzhen University
Department Health Science Center
Street address 3688 Nanhai Ave
City Shenzhen
ZIP/Postal code 518060
Country China
 
Platform ID GPL21273
Series (1)
GSE109280 Boosting ATM activity alleviates ageing and extends lifespan in a mouse model of progeria.
Relations
BioSample SAMN08369646
SRA SRX3585740

Supplementary file Size Download File type/resource
GSM2936421_Sirt6-ko-3-RC-SVmerge.txt.gz 362.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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