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Sample GSM3560206 Query DataSets for GSM3560206
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
 
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

Supplementary file Size Download File type/resource
GSM3560206_T47D_si1_2.expr.txt.gz 33.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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