|
| Status |
Public on Mar 15, 2023 |
| Title |
S.6069.rep1 |
| Sample type |
SRA |
| |
|
| Source name |
7-day-old seedlings with roots
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 7-day-old seedlings with roots
genotype: 6069
|
| Treatment protocol |
no treatment
|
| Growth protocol |
22 degrees Celcius, on soil, long-day conditions (16h light, 8h dark)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated and DNAse I (NEB) treated using a KingFisher Robot with an in-house magnetic RNA isolation kit. RNA was diluted in nuclease free water (Ambion) and stored at -80oC.
TruSeq Stranded mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
150bp PE
TPMs.4_tissues.our_annotation.bed
TPMs.4_tissues.Araport11_annotation.bed
|
| Data processing |
raw RNA-seq reads were aligned to the TAIR10 genome using STAR (v.2.7.1.). First the genomebuild was performed for TAIR10 accounting for the genome size and not providing the annotated splice junctions. The genomebuild command: STAR --runMode genomeGenerate --genomeSAindexNbases 12.5 --genomeDir $stargenomedir --genomeFastaFiles genome.fasta . The command used for alignment: STAR --readFilesIn $fastq.gz --readFilesCommand zcat --runThreadN 4 --alignIntronMax 6000 --alignMatesGapMax 6000 --genomeDir $stargenomedir --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverReadLmax 0.1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMultimapNmax 10 --outReadsUnmapped None --alignSJoverhangMin 8 --outSAMattributes NH HI AS nM NM MD jM jI XS --outSAMtype BAM SortedByCoordinate --runMode alignReads --twopassMode Basic --outFileNamePrefix $out
read counts were calculated using featurecounts from the subread package (v.2.0.0). Command used: featureCounts -T 4 -p -F SAF -O -s 2 -t exon -g gene_id -a $saf -o $out.txt $bam
TPMs were calculated by dividing the raw counts number by the total number of raw counts in the sample (in million reads) and the length (in kb). Command used sum=`cat $out.txt| awk -v OFS="\t" '{ sum += $7} END {print sum}'` cat $out.txt| grep -v Geneid| awk -v OFS="\t" -v sum="$sum" ' {print $1,$6,$7,$7*1000000*1000/($6*sum)}' > $out.counts_tpm.bed
Assembly: TAIR10
Supplementary files format and content: TPMs.4_tissues.our_annotation.bed contains a table with TPMs for 5 gene types in the new annotation (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every RNAseq sample
Supplementary files format and content: TPMs.4_tissues.Araport11_annotation.bed contains a table with TPMs for Araport11 annotated genes and TEs for every RNAseq sample
|
| |
|
| Submission date |
Mar 06, 2023 |
| Last update date |
Mar 15, 2023 |
| Contact name |
Aleksandra Kornienko |
| E-mail(s) |
kornienkoalexandra@gmail.com
|
| Phone |
00431790449000
|
| Organization name |
Gregor Mendel Institute
|
| Lab |
Nordborg
|
| Street address |
Dr. Bohrgasse 3
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE224761 |
Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing |
| GSE226691 |
Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN33596994 |
| SRA |
SRX19573740 |
