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Sample GSM4711206

Query DataSets for GSM4711206

Status

Public on Aug 05, 2023

Title

Trachea.M.1

Sample type

SRA

Source name

hAWO.Mock

Organism

Homo sapiens

Characteristics

tissue: Trachea
treatment: Mock

Extracted molecule

polyA RNA

Extraction protocol

Total RNA in the cells was extracted using Trizol (Invitrogen) according to the manufacturer’s protocol, and 1ug RNA was used to reverse transcribed into cDNA using Oligo (dT). Fragmented RNA (average length approximately 200 bp) was subjected to first strand and second strand cDNA synthesis followed by adaptor ligation and enrichment with a low-cycle according to the instructions of NEBNext" UltraTM RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit"2.0(Life Technologies, USA).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode human transcriptome using RSEM
The gene expression level was calculated by using RSEM
Reads were aligned to the mouse reference genome hg38 with bowtie2, and RSEM was used to quantify the reads mapped to each gene. Gene expression was normalized by EDASEQ. Differentially expressed genes were obtained using DESeq2 (version 1.10.1), a cutoff of Q-value < 0.05 and log2 (fold-change) > 1 was used for identify differentially expressed genes. All differentially expressed mRNAs were selected for GO analyses clusterProfiler. Other analysis was performed using glbase
Genome_build: hg38

Submission date

Aug 05, 2020

Last update date

Aug 05, 2023

Contact name

Jiangping He

E-mail(s)

he_jiangping@grmh-gdl.cn

Organization name

Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

Street address

Kai yuan avenue 190