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Sample GSM2785413

Query DataSets for GSM2785413

Status

Public on Jan 11, 2018

Title

FB1xFB2_8dpi_3

Sample type

SRA

Source name

infected plant material, 8 days post infection

Organisms

Zea mays; Mycosarcoma maydis

Characteristics

host plant variety: EGB
fungal strain: FB1 x FB2
host tissue: leaves
time point: 8 days post infection

Growth protocol

Ustilago maydis strains FB1 and FB2 were grown to OD600=1.0 in YEPSL, pelleted and resuspended in water. The compatible strains were mixed in equal quantities and injected into 7-day-old maize seedlings.

Extracted molecule

total RNA

Extraction protocol

For each sample, leaf sections from 10 different plants infected with FB1 x FB2 U. maydis wild type strains were collected, pooled and frozen in liquid nitrogen. Samples were ground to a fine powder in liquid nitrogen and total RNAs were extracted using the TRIzol method (Invitrogen).
Sequencing libraries were prepared with the Illumina TruSeq stranded mRNA library Prep Kit starting from 2µg total RNA.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

Sample 21
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

Data processing

Reads were quality-filtered (PhredScores lower 20), trimmed for the TruSeq adapters and statically trimmed 12 nucleotides at the 5’ end. Reads smaller than 50 nucleotides were discarded. When the paired-end reads did overlap with at least 10 nucleotides, they were merged to single reads. All analysis was performed using the CLC Genomics Workbench v8.5 (CLC Bio-Qiagen).
For the U. maydis analysis, all reads were filtered against the maize genes (90% identity over 80% of the sequence) and only un-mapped reads were mapped against the U. maydis genes (80% identity over 60% of the sequence). Mapping was performed using the CLC Genomics Workbench v8.5 (CLC Bio-Qiagen).
For the Z. mays analysis, all reads were filtered against the U. maydis genes (90% identity over 60% of the sequence) and only un-mapped reads were mapped against the Z. mays genes (90% identity over 80% of the sequence). Mapping was performed using the CLC Genomics Workbench v8.5 (CLC Bio-Qiagen).
For the U. maydis analysis, all unique exon read counts of the samples 1-24 were normalized using DESeq2 v1.10.
For the Z. mays analysis, all unique exon read counts of the samples 3-45 were normalized using DESeq2 v1.10.
Genome_build: The U. maydis reference genome was from NCBI (https://www.ncbi.nlm.nih.gov , accession numbers NC_026478.1 - NC_026500.1, NW_011929455.1 - NW_011929458.1, NC_008368.1).
Genome_build: The Z. mays reference genome was from Ensembl (http://plants.ensembl.org/info/website/ftp/index.html Zea_mays.AGPv3.28.dna.toplevel).
Supplementary_files_format_and_content: *txt: Tab-delimited text files containing total number of unique exon counts for each U. maydis gene (Counts_Um.txt), DESeq2-normalized counts for each U. maydis gene (NormCounts_Um.txt), total number of unique exon counts for each Z. mays gene (Counts_Zm.txt), DESeq2-normalized counts for each Z. mays gene (NormCounts_Zm.txt).

Submission date

Sep 14, 2017

Last update date

May 15, 2019

Contact name

Clement Pellegrin

Organization name

University of Cambridge

Department

Plant Sciences

Street address

Downing Site