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In our continuous efforts to enhance the efficiency of our services, we've introduced a dedicated **single cell library details** sheet for single-cell projects within our [project registration form](https://www.mdc-berlin.de/genomics#t-nextgenerationsequencing). Given the expanding range of workflows from [10X Genomics](https://www.10xgenomics.com/support), we understand that registering your project might seem daunting. This guide is designed to simplify that process for you.
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In our continuous efforts to enhance the efficiency of our services, we've introduced a dedicated **single cell sheet** for single cell projects within our [project registration form](https://www.mdc-berlin.de/genomics#t-nextgenerationsequencing). Given the expanding range of workflows from [10X Genomics](https://www.10xgenomics.com/support), we understand that registering your project might seem daunting. This guide is designed to simplify that process for you.
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> #### [Project Registration sheet](/Project-Registration-sheet)
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> #### [Libraries transfer sheet](Libraries-transfer-sheet)
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> #### [Single cell sheet](/Single-cell-sheet)
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## Why a Dedicated Library Annotation Sheet?
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The diverse workflows of 10X Genomics require specific annotations to ensure accurate and streamlined analysis. By providing a dedicated annotation sheet, we aim to:
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| ... | ... | @@ -12,23 +19,6 @@ The diverse workflows of 10X Genomics require specific annotations to ensure acc |
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3. **Refer to Dropdown Menus**: Some fields have dropdown menus for standardized responses. Make sure to select the appropriate option.
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4. **Double-Check Your Entries**: Before submitting, review all the information to ensure its accuracy.
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### Project Registration sheet
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Under "data processing and delivery" the following form fields are relevant for us.
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| Field | Options | |
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|-------------------------------------------|-------------------------------------------------------------|---------------------------------------------------------------|
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| raw data required | yes ; no | If yes, we provide per lane basecalls data as *.tar (see [data fromats](/Data-delivery-formats)) |
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| fastq data required | yes ; no | If yes, we will provide fastq.gz, md5sums and basic QC output (see [data fromats](/Data-delivery-formats)) |
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| cell ranger (single-cell projects) | required; <br/> done by CUBI;<br/> not required (done independently) | If required, we will provide cellranger output. If done by CUBI, please add the appropriate mail account to the data receivers |
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| who should get the data, e-mail addresses | All accounts that need to have data access. | We will send a delivery mail and grant access for these accounts. |
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### Libraries transfer sheet
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This sheet contains the library information, used by the NGS team and the DM team. For us, relevant fields are the following.
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| Field | e.g. | |
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|--------------------|-------------------------------------------|------------------------------------------------------------------------------------------------------------------------|
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| pool name | P1234 | Should only contain the NGS project ID (PID). |
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| Library Code/Name | libA_dex_treated_rep1;<br/> SP123_001_wildtype | Can be any library name;<br/> Avoid whitespaces and special characters and separate parts of the name using underscore "_". For libraries processed by the Single Cell Team the nomenclature starts with the single cell project ID (SPID, e.g. SP123) followed by a unique number (e.g. 012)|
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| final name | P1234_SP123_012_wildtype | **Do not fill** this field its combined from "pool name" and "Library Code/Name" field.<br/> How to structure a library name:<br/> - PID_SPID_SPNumber (minimum, e.g. P1234_SP123_004)<br/> - PID_SPID_SPNumber_LibraryType (good, e.g. P1234_SP123_004_GEX) <br/> - PID_SPID_SPNumber_LibraryType_LibraryName (best, e.g. P1234_SP123_004_GEX_Liver01) |
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## Need Assistance?
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If you encounter any challenges or have questions while filling out the form for a specific project, please don't hesitate to contact the members of the [Single-cell](https://www.mdc-berlin.de/genomics#t-single-celltechnologies) or [NGS](https://www.mdc-berlin.de/genomics#t-nextgenerationsequencing) team you are already in contact with. |
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