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Sample GSM5417021

Query DataSets for GSM5417021

Status

Public on Dec 07, 2021

Title

ILS, rep2

Sample type

SRA

Source name

lesion tissue

Organism

Homo sapiens

Characteristics

developmental stage: infant
condition: ILS
tissue: lesion tissue

Extracted molecule

total RNA

Extraction protocol

lesion and normal lung control tissue were removed, flash frozen on dry ice, and RNA was harvested using miRNeasy Mico Kit(QIAGEN 217084).
The strand-specific RNA-seq libraries were prepared using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Vazyme #NR601) following the manufacturer’s instructions.

Library strategy

ssRNA-seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Description

gene_all_counts.csv
gene_all_fpkm.csv
WLFZZ_BB

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, then mapped to GRCh38, version 23(Ensembl 81) using TopHat v2.0.9
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. 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.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

Submission date

Jul 03, 2021

Last update date

Dec 07, 2021

Contact name

jiwen cheng

E-mail(s)

[email protected]

Organization name

Xi'an Jiaotong University

Street address

Xiwu Road