|
Status |
Public on Jan 01, 2020 |
Title |
Si-TINCR-1 rep2 |
Sample type |
SRA |
|
|
Source name |
T47D
|
Organism |
Homo sapiens |
Characteristics |
treatment: si-TINCR
|
Treatment protocol |
Human breast cancer cell lines T47D was seeded in 6-well dishes the night before to give 60-70% confluence for plasmid and 40-50% for miRNA or siRNA transfection. Cells were transfected using Lipofectamine 2000 (invitrogen), according to the manufacturer’s instructions in the following day. At 48 h post-transfection, cells were harvested for qRT-PCR analysis.
|
Growth protocol |
Human breast cancer cell lines T47D was obtained from the Chinese Academy of Sciences Cell Bank and Cellbio (China) and cultured and stored according to their instructions.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was harvested using Trizol reagent RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
BGISEQ-500 |
|
|
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, Bowtie2 is used to map clean reads to the reference genome Homo sapiens GRCh38.p12 and to other sRNA databases. Bowtie2 : -q -L 16 --phred64 -p 6 The small RNA expression level is calculated by using Transcripts Per Kilobase Million (TPM[14]). The TPM method eliminates the influence of sequencing discrepancy on the calculation of small RNA expression level. Therefore, the calculated gene expression level datacanbeuseddirectly tocomparethedifferenceingeneexpressionbetweenthe samples. To calculate the TPM the following formula is used,C means miRNA counts numberis asample,N means totalreads numberthatmappedtogenome: TPM=C*1000000/N Genome_build: GRCh38.p12 Supplementary_files_format_and_content: text files include TPM values for each Sample
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|
|
Submission date |
Jan 11, 2019 |
Last update date |
Jan 02, 2020 |
Contact name |
Jian Wang |
E-mail(s) |
wangjian8@genomics.cn
|
Organization name |
Northeast Agricultural University
|
Street address |
600 Changjiang Road
|
City |
Harbin |
ZIP/Postal code |
150030 |
Country |
China |
|
|
Platform ID |
GPL23227 |
Series (1) |
GSE124961 |
Identification of a novel TINCR-EGFR signaling pathway loop which initiates receptor tyrosine kinases cascade and confers tumorigenesis in human cancer |
|
Relations |
BioSample |
SAMN10726686 |
SRA |
SRX5242435 |