|
| Status |
Public on Mar 24, 2020 |
| Title |
149RS30 |
| Sample type |
SRA |
| |
|
| Source name |
fully expanded leaves
|
| Organism |
Brachypodium distachyon |
| Characteristics |
genotype: phyC
cultivar: Bd21-3
tissue: fully expanded leaves
photoperiod: LD (20 h light/4 h dark)
temperature: 20ºC
replicate: single
time: collected after 2 weeks at ZT20
|
| Growth protocol |
Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT20 by snap-freezing in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Mini Kit (74104) was used to extract RNA. RNA quality and integrity were assessed on the Agilent 2200 TapeStation system.
Library preparation was performed with 1µg total RNA using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420L). The libraries were sequenced on a NextSeq500 (Illumina) running a final pooled library. Each pool contained 24 to 30 samples and was sequenced using NextSeq® 500/550 High Output Kit v2 (150 cycles) TG-160-2002 on a NextSeq500 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
genome build: Bd21-v3.1
NOTE: This sample was processed using spiper with https://github.com/shouldsee/pipeline-rnaseq-hisat2-stringtie/tarball/0.0.2
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15".
Raw reads were aligned with Hisat2 with arguments "--no-mixed --rna-strandness RF --dta --fr" to produce a SAM file.
Duplicate reads were removed with Picard using default setting
Alignments in SAM file were assembled into transcripts abundances with stringtie with argument "--rf".
Supplementary_files_format_and_content: .stringtie.count.txt: TSV table containing abundance of transcripts with bed-formatted coordinates.
Supplementary_files_format_and_content: _bam.bw: Raw coverage bigwig files
Supplementary_files_format_and_content: .cpm.bw: CPM(Count-per-million) normalised bigwig files
|
| |
|
| Submission date |
Mar 23, 2020 |
| Last update date |
Mar 25, 2020 |
| Contact name |
Philip Wigge |
| E-mail(s) |
[email protected]
|
| Organization name |
Cambridge University
|
| Department |
Sainsbury Laboratory
|
| Street address |
47 Bateman street
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1LR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL23254 |
| Series (1) |
| GSE147373 |
RNA-Seq profiling of ELF3 and PRR37 in Brachypodium Distachyon |
|
| Relations |
| BioSample |
SAMN14426771 |
| SRA |
SRX7968928 |
