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Sample GSM4276233

Query DataSets for GSM4276233

Status

Public on Apr 01, 2020

Title

SK225

Sample type

SRA

Source name

pancreatic beta cell

Organism

Sus scrofa

Characteristics

age: embryonic day 40
tissue: pancreas
cell type: beta cell

Extracted molecule

total RNA

Extraction protocol

Cells were removed from pacreatic tissue, and RNA was harvested using RecoverAll Total Nucleic Acid Isolation kit. Takara SMARTer Stranded Total RNA-Seq Kit v2 (Cat# 634413) was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA-Seq Kit protocol. Libraries were multiplexed and sequenced on NextSeq to generate 75bp PE reads.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

SK225

Data processing

Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference transcriptome using Salmon v0.11.3 with parameters salmon quant -i $salmon_index -l A \-1 $Input1 \-2 $Input2 \ p 8 -o quants/${Input1}_quant \ --gcBias –seqBias
Transcripts Per Million (TPM) were calculated using Salmon algorithm from Patro et al., Nat Methods, 2017.
Genome_build: Sus Scrofa reference transcriptome (Sscrofa 11.1, version 96)
Supplementary_files_format_and_content: "normalizedCounts_TPM" include TPM values for each Sample.

Submission date

Jan 17, 2020

Last update date

Apr 01, 2020

Contact name

Seung Kim

E-mail(s)

[email protected]

Organization name

Stanford University

Department

Developmental Biology