|
| Status |
Public on Mar 28, 2018 |
| Title |
PrrX1_KO-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT549
cell type: breast cancer
genotype/variation: PRRX1 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
all_samples_rpkm&RC.txt
PrrX1_KO1
|
| 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
|
| |
|
| 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 |
SAMN08799596 |
| SRA |
SRX3851527 |
