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Sample GSM4870684

Query DataSets for GSM4870684

Status

Public on Dec 25, 2022

Title

srna-19

Sample type

SRA

Source name

SAM(V1)

Organism

Zea mays

Characteristics

age: V1
cultivar: B73

Treatment protocol

No special treatment.

Growth protocol

Twenty-six tissues or stages were sampled from B73 maize plants in a greenhouse. The plants were cultivated under a 12-h light/12-h dark cycle at 25 ℃.

Extracted molecule

total RNA

Extraction protocol

Three replicates were prepared per tissue. RNA was extracted from 5–10 individual plants per replicate. Equal amounts of the three replicates were used for sequencing. Total RNA was isolated from the 26 tissues using a Direct-zol RNA Microprep kit (Zymo Research) following the manufacturer’s guidelines.
RNA libraries were prepared for sequencing using corresponding standard protocols.

Library strategy

ncRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

BGISEQ-500

Description

sRNA-TPM.txt
small RNA

Data processing

Quality control: Raw RNA-seq and circRNA-Seq data were processed by SOAPnuke1.6.548 with the parameters “-n 0.01 -l 20 -q 0.3 -A 0.25” and used SOAPnuke1.6.548 filters RNA to process the raw sRNA-Seq data with the parameters “-p 1 -z 18 -s -Q 2 --sanger”. Ribo-Seq data was removed adaptors and controled low quality by FASTX_Toolkit-0.0.14 fastx_clipper with the parameters "-l 5 -c -n -v -Q33" and fastx_trimmer with the parameters "-f 1 -Q 33".
Alignment: Clean reads were aligned to the maize AGPv4 reference genome. Total RNA-seq data from the 26 tissues or stages were mapped to the B73 AGPv4 reference genome using the default parameters of HISAT and StringTie; small RNAs which size were 18–26 nt were mapped to the maize AGPv4 reference genome using Bowtie-1.1.2 with the parameters unique location and no mismatch; the Ribo-Seq reads were aligned to the rRNA reference sequence using Bowtie-1.1.267 to filter out reads derived from rRNAs and retained reads were mapped to the maize AGPv4 reference genome.
Identification of non-coding RNA: Mapsplice-v2.1.8 was used to identify fusion RNAs from total RNA-seq data from each tissue; and improved version of LncRNA_Finder was used to identify lncRNAs from total RNAs. CIRI v2.0.5 was used to identify circRNAs by aligning them to the maize AGPv4 reference genome.
Quantification of RNA: Total RNAs including lncRNAs and mRNAs bound by ribosome were calculated expression by RSEM. CIRCexplorer2 v2.0.1 was used quantify the expression levels of the circRNAs. The expression of fusion RNA and small RNA was calculated according to the TPM standard formula.
PPIs: The libraries were sequenced on the PacBio platform, and Circular Consensus Sequencing reads were called using SMRTLink-5.1.0.26412. The following analysis was performed to obtain PPIs: Firstly, reads in FASTA format were extracted from BAM files using SAMtools-1.9. Next, because ten barcoded samples were combined to generate each sequencing library, reads from each sample were divided based on their barcode sequences using Cutadapt-1.9.1. Parameters -e and -m for running reads separation were 0.3 and 200, respectively. The reads were aligned to the coding sequence data from the maize AGPv4 genome to identified candidate PPI genes using BLAST+/2.7.1. Only PPI genes with BLAST e-value < 1.0e−4 that matched to two genes were retained. If a CCS contained sequences from two different genes, and the primer sequence and the recombination sequence were aligned consistently, the proteins encoded by the two genes were considered to be interacting proteins.
Genome_build: Zea_mays.B73_RefGen_v4
Supplementary_files_format_and_content: tab-delimited text files named "TPM" or "CPM" include expression values for each samples.
Supplementary_files_format_and_content: tab-delimited text files named "PPIs" include identified protein-protein interactions.

Submission date

Oct 28, 2020

Last update date

Dec 25, 2022

Contact name

qian lin han

Organization name

Huazhong Agricultural University

Street address

Huazhong Agricultural University, No.1 Shizishan Street, Hongshan District

City

wuhan