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Sample GSM5910141

Query DataSets for GSM5910141

Status

Public on Oct 04, 2022

Title

Soy Leaf 400pg Rep 1

Sample type

SRA

Source name

Soy leaf

Organism

Glycine max

Characteristics

strain: Wm82
technique: smar2C2
tissue: Leaf

Growth protocol

Plants grown for four weeks with standard 16H daylight conditions at room temperature

Extracted molecule

polyA RNA

Extraction protocol

RNA was extracted using Monarch Total RNA Extraction and Purification kit (NEB #T2010)
Libraries where prepared using the novel smar2C2 method described in the related manuscript

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Sequences were quality trimmed and adaptors were identified and filtered using CutAdapt v2.8
UMI sequences were extracted from processed fasta files using UMI-tools v1.0.1
Sequences were aligned to their respective genome using STAR v2.7.2
Sequences were deduplicated using the UMI and mapping location using UMI-tools v1.0.1
Transcriptoinal start sites were determined using the R library TSRchitect v1.2.0 in R v4.0.0
Genome_build: Maize genome = AGPv4.38, Sorghum genome = NCBIv3.52, Rice genome = IRGSP-1.0.51, Wheat genome = IWGSC.51, Soy genome = Wm82.a4.v1
Supplementary_files_format_and_content: Text file containing single nucleotide position of transcription start site, read count, and strand

Submission date

Feb 22, 2022

Last update date

Oct 04, 2022

Contact name

Robert J Schmitz

E-mail(s)

[email protected]

Organization name

University of Georgia

Department

Genetics