 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 29, 2019 |
| Title |
dme-7/+ pollen RNA-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
dme-7/+ pollen
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cell type: whole pollen
genotype: dme-7/+
|
| Growth protocol |
plants were grown in LD condition (16h lights/8h darkness) at 22-24 degrees
|
| Extracted molecule |
total RNA |
| Extraction protocol |
follow the instruciton of RNeasy plant micro kit
follow the instructions of Ovation RNA-Seq Systems
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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: rpkm.log2.gff and abundance.tsv
|
| |
|
| Submission date |
Jan 22, 2019 |
| 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 |
GPL19580 |
| Series (1) |
| GSE120519 |
Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation |
|
| Relations |
| BioSample |
SAMN10788494 |
| SRA |
SRX5278259 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3574401_dme7_pollen_rep1_abundance.tsv.gz |
334.5 Kb |
(ftp)(http) |
TSV |
| GSM3574401_dme7_pollen_rep1_w50.rpkm.log2.gff.gz |
2.4 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
