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Sample GSM2509829

Query DataSets for GSM2509829

Status

Public on Dec 05, 2017

Title

MB_09_EM_rep3

Sample type

SRA

Source name

09DAP Embryo

Organism

Zea mays

Characteristics

age: 09DAP
tissue: 09DAP_Embryo
genotype: Mo17xB73

Treatment protocol

This was followed by two kinds of treatments during the pollination:(1) the B73 inbred lines as the female treatment, before pollination, the ear of B73 and the tassel of Mo17 were bagged with kraft paper on the day before pollination. The next day, each paper bag of Mo17 was patted to collect the pollens to pollinate the ear of B73. (2) the Mo17 inbred lines as the female treatment, before pollination, the ear of Mo17 and the tassel of B73 were bagged with kraft paper on the day before pollination. The next day, each paper bag of B73 was patted to collect the pollens to pollinate the ear of Mo17.

Growth protocol

The two inbred lines B73 and Mo17 were grown in the China Agriculture university experiment station of Beijing, and they were used as two parental lines for reciprocal crosses. Before pollination, the ear and the tassel of B73 and Mo17 were bagged with kraft paper on the day before pollination. The next day, each paper bag was patted to collect the pollens from one parental, which were used to pollinate the ear of the other parental.

Extracted molecule

total RNA

Extraction protocol

As described above, 15 kinds of embryo samples and one endosperm sample were collected for RNA-seq analysis. For each sample, hundreds(9DAP,11DAP,13DAP) or thousands(5DAP,7DAP) individual embryos were put into one tube containing RNA storing liquid buffer (Hueyueyang, China) (three replicates). The embryo and endosperm were collected from at least three ears in each replicate. RNA samples were isolated by Quick RNA isolation Kit (Huayueyang, China) and were checked on 1% agarose gels to avoid possible degradation and contamination. Then examined by a Nano Photometer spectrophotometer (IMPLEN, CA, USA) for RNA purity and sent to the Novogene for mRNA library construction and high-throughput sequencing using the Illumina HiSeq2500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

Sample_rawcounts_FPKM.xls

Data processing

Illumina Casava1.7 software used for basecalling.
The clean reads (quality checked by FastQC) were aligned to the reference genome twice. At first, clean reads were mapped to B73 reference using Tophat aligner(with 4 mismatch) and the unmapped reads were remapped to SNPs-substituted reference (B73 reference substituted to MO17 reference by replacing SNPs between B73 and MO17) using the Tophat aligner (with 2 mismatches). Reads with no more than five best mapped positions were retained for further analysis. After combining above mapping results, read counts of annotated genes (filtered gene set version 5b.60) were summarized by HTSeq-count. Gene expression [Reads per kilobase of transcript per million fragments mapped] (FPKM) was estimated by Cufflinks (V2.2.1) software.
Genome_build: REL5b.60
Supplementary_files_format_and_content: Tab-delimited text file include Reads and FPKM values for 48 Samples .

Submission date

Feb 27, 2017

Last update date

May 15, 2019

Contact name

Cheng Zhao

E-mail(s)

[email protected]

Organization name

Karolinska institute

Department

Clinical Science