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Sample GSM8060193

Query DataSets for GSM8060193

Status

Public on Feb 10, 2024

Title

HEK293_siZC3H14_polyA

Sample type

SRA

Source name

HEK293 cells

Organism

Homo sapiens

Characteristics

cell line: HEK293 cells
genotype: WT

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) followed by RNase R treatment or not according to the manufacturer’s instructions.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

ZC3H14_KD_polyA-tail.txt.gz

Data processing

The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the reference genome with Bowtie2. For linear RNAs, the corresponding reads were counted with BEDtools and read per million (RPM) was used to calculate levels. For circRNA annotation, CIRI2 and Find_circ were used, and backspliced read per million (BRPM) was used to calculate circRNA levels.
Assembly: hg19 (human), mm10 (mouse) and ASM294v2 (yeast)
Supplementary files format and content: tab-delimited text files include reads for each Sample

Submission date

Feb 02, 2024

Last update date

Feb 10, 2024

Contact name

Xiaolin Wang

E-mail(s)

wxl20089@mail.ustc.edu.cn

Phone

15155979787

Organization name

USTC