| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
ERR841782 |
11.2M | 558.6Mbp | 374.9M | 51.1% | 2015-04-16 | public |
This run has 2 reads per spot:
| L=50, 100% | L=0 |
- 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 | 2015-04-15 |
| ENA-LAST-UPDATE | 2018-11-16 |
| Experiment | Library Name | Platform | Strategy | Source | Selection | Layout | Action |
|---|---|---|---|---|---|---|---|
| ERX921844 | Sample 6 | Illumina | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE |
Design:
| Biosample | Sample Description | Organism |
|---|---|---|
| SAMEA3321801 (ERS696584) | Protocols: total 8 does were weighed and premedicated with ketamine 50 mg/kg kg (Ketamine 1000 CEVA; CEVA Sante Animale, Brussels, Belgium), xylazine 6 mg/kg (Vexylan; CEVA Sante Animale), and Buprenorphine 0.03 mg/kg (Vetergesic; Reckitt Benckiser Healthcare, Brussels, Belgium), all injected intramuscularly. General anesthesia was maintained using a face mask with isoflurane 1.5% (Isoba Vet; Abbott Laboratories Ltd., Queenborough, Kent, UK) in oxygen at 1 L/min. Maternal heart rate and oxygen saturation were monitored with a pulse oxymeter (Nellcor N-20P; Nellcor Inc., Haasrode, Belgium). Body temperature was maintained by a heating pad. The doe was placed in the supine position, the abdominal wall was shaved and disinfected with povidone iodine (Isobetadine; Asta Medica, Brussels, Belgium) and draped in a sterile fashion. Throughout all surgical procedures aseptic conditions were maintained. In every doe we operated on two fetuses each in the middle of the left or right uterine horn. First diaphragmatic hernia (DH) was created at 23 days' GA. A second operation was performed on these DH fetuses at 28 days' GA. At that time, one fetus underwent tracheal occlusion (TO group), whereas another underwent a sham operation (DH group), i.e. hysterotomy, fetal neck exposure, tracheal dissection without ligation, and skin closure. The latter is performed to exclude the effects of a fetal surgical procedure per se. At 30 days' GA, the does were euthanized and all operated fetuses and 1 control nonoperated littermate (WT) were harvested by cesarean section to obtain nonventilated lungs. total 8 does were weighed and premedicated with ketamine 50 mg/kg kg (Ketamine 1000 CEVA; CEVA Sante Animale, Brussels, Belgium), xylazine 6 mg/kg (Vexylan; CEVA Sante Animale), and Buprenorphine 0.03 mg/kg (Vetergesic; Reckitt Benckiser Healthcare, Brussels, Belgium), all injected intramuscularly. General anesthesia was maintained using a face mask with isoflurane 1.5% (Isoba Vet; Abbott Laboratories Ltd., Queenborough, Kent, UK) in oxygen at 1 L/min. Maternal heart rate and oxygen saturation were monitored with a pulse oxymeter (Nellcor N-20P; Nellcor Inc., Haasrode, Belgium). Body temperature was maintained by a heating pad. The doe was placed in the supine position, the abdominal wall was shaved and disinfected with povidone iodine (Isobetadine; Asta Medica, Brussels, Belgium) and draped in a sterile fashion. Throughout all surgical procedures aseptic conditions were maintained. In every doe we operated on two fetuses each in the middle of the left or right uterine horn. First diaphragmatic hernia (DH) was created at 23 days' GA. A second operation was performed on these DH fetuses at 28 days' GA. At that time, one fetus underwent tracheal occlusion (TO group), whereas another underwent a sham operation (DH group), i.e. hysterotomy, fetal neck exposure, tracheal dissection without ligation, and skin closure. The latter is performed to exclude the effects of a fetal surgical procedure per se. At 30 days' GA, the does were euthanized and all operated fetuses and 1 control nonoperated littermate (WT) were harvested by cesarean section to obtain nonventilated lungs. RNA isolation was performed on the whole left lung samples within 4hrs of harvesting using the RNeasy mini kit (Qiagen Benelux B.V., Venlo NL ). Tissue lysis and homogenization was performed in 1200ul Buffer RLT using the TissueLyser system (Qiagen Benelux B.V., Venlo NL). One ug of total RNA was used as input material for sequencing library preparation which was performed with the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturers protocol. Fragmentation was performed for 6 mins. 8 PCR cycles were used for PCR enrichment step. Samples were indexed to allow for multiplexing. | Oryctolagus cuniculus |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJEB9024 | ERP010078 | Rabbit Lung_DH_TO_Control |
Investigation into the effects of Congenital Diaphragmatic Hernia (CDH) and subsequent treatment with tracheal occlusion (TO) on the pulmonary transcriptome. A diaphragm defect was created by surgical means in fetal rabbits. The surgical creation of diaphragmatic hernia (DH) allows for direct analysis of changes in pulmonary gene expression due to pulmonary hypoplasia, without the need for gene knockdown (as for KO mice) or use of teratogens (such as nitrofen). The subsequent treatment with tracheal occlusion (TO) was also investigated to determine the changes in gene expression due to forced lung growth in the prenatal phase. RNA-Seq analysis was performed on left lung samples from fetal rabbits. Samples were generated and analysed for DH (n=4), TO (n=6), and control lungs (n=4)
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 | 366,154 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/ERR841782/ERR841782 | worldwide | anonymous |
| SRA Lite | 138,105 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/ERR000/841/ERR841782/ERR841782.lite.2 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-9/ERR841782/ERR841782.lite.2 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-106/ERR841782/ERR841782.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 | 524,409 Kb | AWS | s3://sra-pub-src-16/ERR841782/GC003015.PB_RNAseq121002.lane5.121015FCB.fastq.gz.1 | - | Use Cloud Data Delivery |
| EBI | http://ftp.sra.ebi.ac.uk/vol1/run/ERR841/ERR841782/GC003015.PB_RNAseq121002.lane5.121015FCB.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
- gs.US is free to access from machines running in Google’s gs.US region, access from other regions or transport outside of GCP will require paying egress charges
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: 67.47%
- Identified reads: 32.53%
Strong signals
| SuperKingdom | Organism | Rank | %% | Kbp | Coverage |
|---|---|---|---|---|---|
| Eukaryota | Oryctolagus cuniculus | species | 32.2 | 179,801 | |
| Bacteria | Bacteria | superkingdom | 0.2 | 912 | |
| Viruses | Microviridae | family | 0.0 | 25 |
- 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