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Sample GSM2835777

Query DataSets for GSM2835777

Status

Public on Oct 30, 2020

Title

shTBX3 rep2

Sample type

SRA

Source name

thyroid cancer

Organism

Homo sapiens

Characteristics

cell line: K1
tissue: thyroid cancer
genotype: TBX3 knockdown

Growth protocol

Cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using Trizol reagent. First Strand cDNA Synthesis Kit (04 896 866 001, Roche) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

BGISEQ-500

Data processing

We use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie2 parameters for SE reads: -q --phred64 --sensitive --dpad 0 --gbar,HISTA parameters for SE reads: -p 8 --phred64 --sensitive -I 1 -X 1000
FPKMs were calculated by RSEM, which is the quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores to determine which transcripts are isoforms of the same gene.
Genome_build: hg19

Submission date

Oct 30, 2017

Last update date

Oct 30, 2020

Contact name

xiaomeng Li

E-mail(s)

[email protected]

Phone

13821030797

Organization name

Tianjin medical university