Description
Material provided: Data
Unit definition: Bioinformatic analysis for:
Library preparation: TruSeq Stranded mRNA
Option 1: 450 million reads for 2×100 Paired End Length
Option 2: 650 million reads for 2×75 Paired End Length
Total RNA-Seq offers invaluable information about the transcriptome, but data analysis is usually the point that causes delays. A plethora of available tools that rely on several similar but not identical algorithms and the great number of statistical models that can be used depending on the questions need to be answered. The Provider (Bioinformatics Support Group at IMBB, FORTH) has significant experience in analysing similar datasets from quality control, genome mapping (if a reference genome is available), transcriptome assembly, differential gene expression, statistical testing and downstream analysis (GO terms assignment and pathway analysis).
The experiment and the product
The Bioinformatics analysis for total RNASeq service, includes the following for each sample:
- Quality control of the input data from the sequencing
- Pre-processing of the reads (removing adaptors if any, quality trimming)
- Mapping to a reference genome (if available)
- Transcriptome assembly (if needed)
- Identification of differentially expressed genes (if needed)
- Downstream analysis
End-user responsibilities
Provide data
Raw NGS data in the form of .fastq files, detailed description of the experiment/material used (e.g. if any batch effect is expected, if samples came from the same (pool of) animal(s) or not and details about the libraries used for sequencing.
– Remarks
- a) if the provided data fail during quality control the customer will be contacted to discuss the nature of the problem and resolve it before initiating any analysis.
Dispatch of samples
You can send us the link to download directly from the sequencing unit the raw data or, you can contact us to provide a way to upload the data to our servers. If you prefer you can send us your data in an external storage device.
– Remarks
- a) to compensate the biological variability within the experiment due to RNA, a biological triplicate for each experimental condition is recommended.
Supplier responsibilities
Storage of biological sample
The provider will store the analyzed samples only for 1 month after delivery. Extended storage time is available for a maximum of 4 months and must be requested in advance of the experiments.
Storage of data
The provider waives any responsibility for the storage and backup of the supplied project and sequencing data after delivery to the end-user. We will store the project data only for 1 month after delivery. After expiration of this period, all data are removed from our servers and archived (unless otherwise agreed with the end-user). Your data might be re-imported at an extra cost within the period of 1 year after delivery of the final data. After 1 year, all project data will be deleted permanently from our systems. Extended data storage is available on request at an extra cost and must be requested at project start.
Delivery of results
The sequencing results will be sent via email or by DVD, USB or hard disk driver, depending on the total amount of data.
Modalities of transfer:
-by “zip attachment” to email for data of up to 10 Mb
-by “wetransfer” service to email for data up to 2 Gb
-by our Google Drive up to 10 Gb
-by HD for data over 10 Gb
Please note that the cost of HD driver is not included. Where requested, the end-user must provide the HD. We can always upload the results to your servers via FTP at no extra cost.
Note: This product offers bioinformatic analysis for RNAseq total transcriptome Illumina sequencing. You can’t order it alone. To order the corresponding sequencing, see associated product.
Total RNA-Seq offers invaluable information about the transcriptome, but data analysis is usually the point that causes delays. A plethora of available tools that rely on several similar but not identical algorithms and the great number of statistical models that can be used depending on the questions need to be answered.
The Provider (Bioinformatics Support Group at IMBB, FORTH) has significant experience in analysing similar datasets from quality control, genome mapping (if a reference genome is available), transcriptome assembly, differential gene expression, statistical testing and downstream analysis (GO terms assignment and pathway analysis).
The experiment and the product
The Bioinformatic analysis for total RNASeq service, includes the following for each sample:
- Quality control of the input data from the sequencing
- Pre-processing of the reads (removing adaptors if any, quality trimming)
- Mapping to a reference genome (if available)
- Transcriptome assembly (if needed)
- Identification of differentially expressed genes (if needed)
- Downstream analysis
End-user responsibilities
Provide data
Raw NGS data in the form of .fastq files, detailed description of the experiment/material used (e.g. if any batch effect is expected, if samples came from the same (pool of) animal(s) or not and details about the libraries used for sequencing.
– Remarks
a) if the provided data fail during quality control the customer will be contacted to discuss the nature of the problem and resolve it before initiating any analysis.
Dispatch of samples
You can send us the link to download directly from the sequencing unit the raw data or, you can contact us to provide a way to upload the data to our servers. If you prefer you can send us your data in an external storage device.
– Remarks
a) to compensate the biological variability within the experiment due to RNA, a biological triplicate for each experimental condition is recommended.
Supplier responsibilities
Storage of biological sample
The provider will store the analyzed samples only for 1 month after delivery. Extended storage time is available for a maximum of 4 months and must be requested in advance of the experiments.
Storage of data
The provider waives any responsibility for the storage and backup of the supplied project and sequencing data after delivery to the end-user. We will store the project data only for 1 month after delivery. After expiration of this period, all data are removed from our servers and archived (unless otherwise agreed with the end-user). Your data might be re-imported at an extra cost within the period of 1 year after delivery of the final data. After 1 year, all project data will be deleted permanently from our systems. Extended data storage is available on request at an extra cost and must be requested at project start.
Delivery of results
The sequencing results will be sent via email or by DVD, USB or hard disk driver, depending on the total amount of data.
Modalities of transfer:
-by “zip attachment” to email for data of up to 10 Mb
-by “wetransfer” service to email for data up to 2 Gb
-by our Google Drive up to 10 Gb
-by HD for data over 10 Gb
Please note that the cost of HD driver is not included. Where requested, the end-user must provide the HD. We can always upload the results to your servers via FTP at no extra cost.
For more information, please contact us.
IMBB Technical Support:
Email: bioinfo@imbb.forth.gr
Telephone: 0030 2810 391159