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Sample GSM3635565

Query DataSets for GSM3635565

Status

Public on Jan 08, 2022

Title

1B rep4 [RNA-Seq]

Sample type

SRA

Source name

Leaf tissue

Organism

Zea mays

Characteristics

genotype: 1B
age: 45-day

Growth protocol

45-day grown in the greenhouse

Extracted molecule

total RNA

Extraction protocol

Extracted by mirVana™ miRNA Isolation Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

EB40

Data processing

For mRNA-seq: 1. the 3' end of the reads was trimmed for Illumina adapters, for ambiguous nucleotides (N's), and for artificial poly-G using cutadapt version 1.16; 2. Low quality reads were removed; 3. ERCC reads were selected and mapped to ERCC references independently; 4. Reads with ERCC removed were mapped to W22 genome v2 using tophat2, then to B73 genome v4 using tophat2, finally to TE sequences using bowtie2; 5. Read counts were normarlized with RPKM; 6. Differential gene expression analysis were performed via edgeR.
For sRNA-seq: 1. the 3' end of the reads was trimmed for Illumina adapters, for ambiguous nucleotides (N's), and for artificial poly-G using cutadapt version 1.16; 2. Low quality reads were removed; 3. Reads were mapped to W22 genome v2 and transposable element seqeunes respectively using shortstack; 4. Read counts were normarlized with RPM; 5. Differential gene expression analysis were performed via edgeR.
Genome_build: W22v2 & TE sequences from W22 genome annotation
Supplementary_files_format_and_content: Tab-delimited text files include raw counts table, normalized counts table, differential gene expression analysis (edgeR) for each sample in mRNA-seq experiments; raw count table of mapped sRNA and RPM counts by ShortStack.
Supplementary_files_format_and_content: Counts_ERCC.txt: raw count table.
Supplementary_files_format_and_content: Counts_miRNA.txt: raw count table by ShortStack.
Supplementary_files_format_and_content: Counts_gene.txt: raw count table.
Supplementary_files_format_and_content: Counts_TE.txt: raw count table.
Supplementary_files_format_and_content: Counts_TE_RPKM.txt: RPKM normalized count table.
Supplementary_files_format_and_content: DGE_analysis.txt: Cuffdiff normalized count table.
Supplementary_files_format_and_content: EdgeR_miRNA.txt: edgeR.
Supplementary_files_format_and_content: EdgeR_TE.txt: edgeR.
Supplementary_files_format_and_content: Counts_miRNA_rpm.txt: RPM normalized count table.

Submission date

Feb 28, 2019

Last update date

Jan 08, 2022

Contact name

Xiaowen Shi

Organization name

Zhejiang University

Department

College of Agriculture and Biotechnology

Lab

Shi Lab