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Sample GSM3402483 Query DataSets for GSM3402483
Status Public on May 29, 2019
Title WT pollen RNA-seq rep5
Sample type SRA
 
Source name WT pollen
Organism Arabidopsis thaliana
Characteristics cell type: whole pollen
genotype: WT
Growth protocol plants were grown in LD condition (16h lights/8h darkness) at 22-24 degrees
Extracted molecule total RNA
Extraction protocol follow the instruction of Mirvana miRNA isolation kit
follow the instructions of ScriptSeq v2 RNA-seq lib prep kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description mikado-permissive.superloci.gff
TAIR10_gene_plus_mikado_TE_transcripts.gff
This sample was used only for TE transcript identification and not the RPKM calculations.
Data processing Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads and 150 base reads were divided in half. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
RNA-Seq: TE transcript annotation was created using four biological replicates of pollen RNA-seq data. Tophat2, Hisat, and STAR were used to align the RNA-seq reads to the TAIR10 genome
Transcripts were assembled using CLASS2, StringTie, and Cufflinks, respectively.
Assembled transcripts were selected by Mikado using default options except the BLAST and Transdecoder steps were disabled. As a result, 21381 transcripts (called superloci) were identified and included in the output file called mikado-permissive.superloci.gff.
The list of superloci was refined by selecting those overlapping with TAIR10 TE annotation.
TE-like genes were eliminated from the refined list if their CG methylation is less than 0.7 in rosette leaves. This gave rise to an annotation of TE transcripts.
The annotation of TE transcripts was combined with TAIR10 gene annotation for Kallisto analysis which gives rise to the output files named abundance.tsv.
Genome_build: TAIR10
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.
 
Submission date Sep 26, 2018
Last update date May 29, 2019
Contact name Xiaoqi Feng
E-mail(s) xiaoqi.feng@jic.ac.uk
Organization name John Innes Centre
Department Cell and Developmental Biology
Lab Xiaoqi Feng
Street address Norwich Research Park
City Norwich
State/province Norfolk
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platform ID GPL13222
Series (1)
GSE120519 Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation
Relations
BioSample SAMN10133531
SRA SRX4741753

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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