Illumina HiSeq 2000 paired end sequencing; High resolution survey of drought, high salinity, heat and cold stress-induced transcriptome of bioenergy feedstock model plant western poplar (Populus trichocarpa) accession Nisqually-1(ERR1864454)
| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
ERR1864454 |
10.6M | 2.1Gbp | 1.4G | 44.9% | 2018-01-11 | public |
This run has 2 reads per spot:
| L=101, 100% | L=101, 100% |
- Legend
Technical read Application Read L=4, 100% Length is 4, 100% spots contain this read ̅L=165, σ=92.8, 66% Average length is 165, standard deviation is 92.8, 66% spots contain this read
| Name | Value |
|---|---|
| ENA-FIRST-PUBLIC | 2018-01-10 |
| ENA-LAST-UPDATE | 2018-11-16 |
| Experiment | Library Name | Platform | Strategy | Source | Selection | Layout | Action |
|---|---|---|---|---|---|---|---|
| ERX1925341 | Root-short-term-cold-replicate-2_p | Illumina | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED |
| Biosample | Sample Description | Organism |
|---|---|---|
| SAMEA102903418 (ERS1575319) | Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in 'PureLink Plant RNA Reagent' (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent' (Thermo Fisher Cat # AM1907), following manufacturer's instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer's protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture's protocol. | Populus trichocarpa |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJEB19784 | ERP021848 | High resolution survey of drought, high salinity, heat and cold stress-induced transcriptome of bioenergy feedstock model plant western poplar (Populus trichocarpa) accession Nisqually-1 |
Abiotic stress is a major factor affecting the growth, development, yield and quality in plants including the important biomass yield such as in a bioenergy feedstock crops. In a first of its kind, RNA-seq based high resolution survey of abiotic stress-induced transcriptome of bioenergy feedstock model plant western poplar (Populus trichocarpa accesion Nisqually-1) was carried out by way of 81 libraries made from total RNA isolated from three tissues, mature vascular leaf, stem xylem and root sampled from plants subjected to untreated control and treated with four individual stress treatments cold, heat, drought and high salinity. For every tissue and treatment type including controls, three individual plants were used per treatment as biological replicates. This research project is supported by the DOE Office of Science, Office of Biological and Environmental Research (BER), USA, grant no. DE-SC0008570
SRA archive data
SRA archive data is normalized by the SRA load process and used by the SRA Toolkit to read and produce formats like FASTQ, SAM, etc. The default toolkit configuration enables it to find and retrieve SRA runs by accession.
Public SRA files are now available from GCP and AWS cloud platforms as well as from NCBI. Access to most data in the cloud requires a user account with the cloud service provider. The user’s account will incur costs for cloud compute or to copy data outside of the specified cloud service region.
| Type | Size | Location | Name | Free Egress | Access Type |
|---|---|---|---|---|---|
| SRA Normalized | 1,362,159 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/ERR1864454/ERR1864454 | worldwide | anonymous |
| SRA Lite | 523,869 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/ERR001/1864/ERR1864454/ERR1864454.lite.2 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-9/ERR1864454/ERR1864454.lite.2 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-104/ERR1864454/ERR1864454.lite.2 | gs.us-east1 | gcp identity |
Original format
The original files submitted to SRA. These files may require specific software to open, read and interpret data.
| Type | Size | Location | Name | Free Egress | Access Type |
|---|---|---|---|---|---|
| fastq | 863,760 Kb | AWS | s3://sra-pub-src-9/ERR1864454/Root_short-term_cold_rep2_F.fastq.gz.1 | - | Use Cloud Data Delivery |
| EBI | http://ftp.sra.ebi.ac.uk/vol1/run/ERR186/ERR1864454/Root_short-term_cold_rep2_F.fastq.gz | worldwide | anonymous | ||
| fastq | 865,855 Kb | AWS | s3://sra-pub-src-9/ERR1864454/Root_short-term_cold_rep2_R.fastq.gz.1 | - | Use Cloud Data Delivery |
| EBI | http://ftp.sra.ebi.ac.uk/vol1/run/ERR186/ERR1864454/Root_short-term_cold_rep2_R.fastq.gz | worldwide | anonymous |
- Egress and Access: what does it mean?
-
Egress
term used by cloud providers to describe cost (charged to the user) of moving data outside of the storage region Free Egresscolumn indicates where the data can be accessed without an egress charge: - worldwide can be downloaded from anywhere for free
- s3.us-east-1 is free to access from machines running in Amazon's us-east-1 region, access from other regions or transport outside of AWS will require paying egress charges
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Access Typedescribes whether a cloud service user account is necessary for data access. "anonymous" access means general public access Namecolumn provides either a link to free download location at NCBI or a URL for the cloud provider storage location. Either s3:// for Amazon or gs:// for Google storage
- Why is SRA data in the cloud?
-
In order to support large scale (hyper parallel) data analyses SRA data is now available at GCP and AWS with few caveats:
- SRA data is copied to the cloud from NCBI. There may be a lag between availability from NCBI and from CSP (cloud service providers)
- To access public data user account with the cloud service provider is required. Your account will incur costs for cloud compute and/or to copy data (either archival or results of your comute) outside of the specified cloud service region
- Distribution of protected data is signed by NIH account and requires user to operate in the same region as the data
SRA has also begun to provide access to originally submitted source files:
- not all files have been validated by SRA
- not all files have been copied to cloud locations (recovering it from NCBI tape system takes time ).
- the volume of this type of data a much larger and it is not used as often so we will keep most of it on tape or "cold" storage in cloud. As a result the data may not be available instantly and restore requests will be served on first-come first-served basis and cost of resore may be charged to your user account.
- What is "Cloud Data Delivery"?
-
Please visit SRA Data Delivery service to request Sequence Read Archive (SRA) data to be delivered to an Amazon Web Services (AWS) or Google Cloud Platform (GCP) bucket of your choice.
Taxonomy Analysis
- Unidentified reads: 11.54%
- Identified reads: 88.46%
Strong signals
| SuperKingdom | Organism | Rank | %% | Kbp | Coverage |
|---|---|---|---|---|---|
| Eukaryota | Populus trichocarpa | species | 86.3 | 1,841,507 | |
| Eukaryota | Populus alba | species | 0.8 | 17,783 | |
| Eukaryota | Populus euphratica | species | 0.6 | 13,456 | |
| Bacteria | Bacteria | superkingdom | 0.6 | 12,584 | |
| Archaea | Thermoplasmatales | order | 0.0 | 299 |
- How to read results?
Results show distribution of reads mapping to specific taxonomy nodes as a percentage of total reads within the analyzed run. In cases where a read maps to more than one related taxonomy node, the read is reported as originating from the lowest shared taxonomic node. So when a read maps to two species belonging to the same genus, it is assigned at the genus level. Sequence reads from a single organism will map to several taxonomy nodes spanning the organism’s lineage. The number of reads mapping to higher level nodes will typically be greater than those that map to terminal nodes.
STAT results are proportional to the size of sequenced genomes. Given a mixed sample containing several organisms at equal copy number, proportionally more reads originate from the larger genomes. This means that the percentages reported by STAT will reflect genome size and must be considered against the genomic complexity of the sequenced sample.
- How can I query this analysis data?
Please take a look at NCBI SRA Cloud-based Taxonomy Analysis Table