|
Status |
Public on Mar 28, 2018 |
Title |
Sirt1_KO-rep2 |
Sample type |
SRA |
|
|
Source name |
breast cancer cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: BT549 cell type: breast cancer genotype/variation: Sirt1 KO
|
Treatment protocol |
SIRT1 and PRRX1 were knocked out by CRISPR-Cas9 procedure in BT549 cells.
|
Growth protocol |
BT549 cells were cultured in RPMI-1640 (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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
|
|
Description |
all_samples_rpkm&RC.txt Sirt1_KO2
|
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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata 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: GRCh38.77 Supplementary_files_format_and_content: text files include RPKM and read count (RC) values for each Sample
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|
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Submission date |
Mar 27, 2018 |
Last update date |
Mar 28, 2018 |
Contact name |
Xiaolong Tang |
E-mail(s) |
terrytang15szu@163.com
|
Organization name |
shenzhen university
|
Street address |
3688 Nanhai Ave, Nanshan District
|
City |
shenzhen |
ZIP/Postal code |
518060 |
Country |
China |
|
|
Platform ID |
GPL20795 |
Series (1) |
GSE112365 |
A SIRT1-centered Circuitry Regulates Breast Cancer Stemness and Metastasis |
|
Relations |
BioSample |
SAMN08799598 |
SRA |
SRX3851525 |