GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2746566

Query DataSets for GSM2746566

Status

Public on Aug 23, 2017

Title

Tfcp2l1 shRNA

Sample type

SRA

Source name

HES_Tfcp2l1 shRNA

Organism

Homo sapiens

Characteristics

cell line: HES2
cell type: human embryonic stem cells
infected with: Tfcp2l1 knockdown lentivirus

Extracted molecule

total RNA

Extraction protocol

Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. BGISEQ-500 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

BGISEQ-500

Data processing

Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from BGI company. 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 of BGI.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

Submission date

Aug 18, 2017

Last update date

May 15, 2019

Contact name

shoudong ye

Organization name

Anhui University

Department

Cell Biology

Street address

No 111, Jiu Long Road