 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 05, 2018 |
| Title |
WT -1 |
| Sample type |
SRA |
| |
|
| Source name |
murine embryonic fibroblast cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: murine embryonic fibroblast cell
genotype: WT
|
| 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 |
SAMN08369651 |
| SRA |
SRX3585735 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2936416_WT-1-RC-SVmerge.txt.gz |
360.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
