Genomics, Sandbox How to order

Sandbox

Sandbox equipment and consumables can ONLY be used by trained Weizmann scientists following a workshop. For any question, contact Hadas Keren-Shaul hadas.keren-shaul@weizmann.ac.il, Tel. 6782 or the Genomics, Sandbox unit, Tel. 9212.

 

Bulk RNA-seq - Mars-seq

Weizmann scientists interested in participating in the Mars-seq workshop should email Hadas Keren-Shaul, hadas.keren-shaul@weizmann.ac.il. Please note that there is a preference for training one person per research group and only he/she will be able to work in the Sandbox unit. It is therefore preferable it will be someone that has substantially a significant amount of time left in the lab.

Workshops are free of charge and limited to 3 participants. Workshops are open for Weizmann students and scientists only, and take place periodically on an approximately once a month schedule. Only workshop graduates will be able to use the sandbox facility.

Up to 192 unique barcodes are available for library prepartion. Prepared libraries can be  be sequenced in the unit's NovaSeq or Aviti sequencers.

Following the workshop, the user will receive instructions on how to reserve the Sandbox facility. In short, a ‘Sandbox’ slot can be reserved through the internal services. The user first needs to open an order in ‘Genomics, Sandbox (order) for the number of samples they wish to process. This will yield an order number which can be used to reserve the Sandbox slot in the desired day and time in‘Genomics, Sandbox (room reservation)’.

Short read Sequencing - NovaSeqX Plus, Illumina

The NovaSeqX is located at the INCPM in the genomics unit (solar tower) and is open for independent Sandbox usage following training.

Weizmann users wishing to use the NovaSeqX Illumina sequencer should coordinate a NovaSeq training with Muriel Chemla, muriel.chemla@weizmann.ac.il, X4435. A basic training / guidance is necessary even if the user is experienced.

The user should be able to provide the following information:

  1. UserID of the User.
  2. UserID of the PI.
  3. Library type (how was it prepared).
  4. Format of illumina parameters required - Rd1, Rd2, i5, i7.
  5. Samples for run should be a pool of ~20 ul at 2 nM.

Few guidelines:

  1. Trained and authorized weizmann users who wish to reserve the NovaSeq should place an internal service order under Genomnics, Sandbox (INCPM NovaSeq). Using the internal service order number, the user can reserve a NovaSeq slot under ‘Genomics, Sandbox (room reservation)’.
  2. If you do not plan to use your sequencing slot, please be considerate and cancel your slot on time as others might need it.
  3. On the day of the NovaSeq sequencing run, 2 hr before you plan to arrive, call the INCPM unit, X5168, and ask to thaw the sequencing kit for you. If seuencing using a 300 cycles kit, call 4 hr before or the night before to allow enough time to thaw. 
  4. After the NovaSeq run had started, and during the time of the run, the user MUST log in to https://ngs-pipeline.weizmann.ac.il/ and register the run. This is critical for data retrieval. Use your weizmann user name and password for login. Once the run is finished, the user will receive an email with a link to his data. For more information about the workflow https://ngs-pipeline.weizmann.ac.il/ngsb/howto

Please note: the user is responsible for the quality of his library and his sequencing results. The Sandbox unit will not be held responsible for any decrease in yield due to sequence biases, low complexity regions or other problems in the library. If you have any questions, you are welcome to contact us or Danyel Biotech (Illumina representatives) directly.

 

Short read sequencing - Aviti, Element Biosciences

Weizmann users wishing to use the Aviti sequencer should contact David Pilzer, david.pilzer@weizmann.ac.il, Tel. 4435.

 

The user should be able to provide the following information:

  1. Library type and library QC
  2. Sequencing parameteres - Rd1, Rd2, i5, i7.
  3. Samples for run should be a pool of ~20 ul at 1 nM.
  4. Prior to sequencing a specific library type for the first time, we will consult with Element Bioscience technical team regarind loading concnetration and optimal running conditions and script.

 

Few guidelines:

  1. Open an internal service order under Genomics, Sandbox for itemcode37 - Aviti Element 2*75 High output. Using the internal service order number, David Pilzer will reserve the instrument for you.
  2. The Aviti training will be a one-on-one personal training.
  3. After the Aivit run had started, and during the time of the run, the user MUST log in to https://ngs-pipeline.weizmann.ac.il/ and register the run. This is critical for data retrieval. Use your weizmann user name and password for login. Once the run is finished, the user will receive an email with a link to his data. For more information about the workflow https://ngs-pipeline.weizmann.ac.il/ngsb/howto
Single cell multiomics - Chromium, 10x Genomics

If you are interested in single cell multiommics using the 10X Genomics technology , please contact Merav Kedmi, merav.kedmi@weizmann.ac.il, Tel. 9212

 

Spatial transcriptomics - Visium, 10x genomics

If you are interested in performing spatial transcriptomics using the 10X Genomics visium technology, please fill in this form: Visium HD 

For any questions, contact Merav Kedmi, merav.kedmi@weizmann.ac.il, Tel. 9212

Bulk ATAC-seq

Weizmann users wishing to perform bulk ATAC-seq should coordinate a meeting with David Pilzer, david.pilzer@weizmann.ac.il, Tel. 4435.

A 2-day trainining for the bulk ATAC-seq protocol will be coordinated.

Following the training, a ‘Sandbox’ slot for bulk ATAC-seq can be reserved through the internal services. The user first needs to open an order in ‘Genomics, Sandbox (order) for itemcode 38, bulk ATAC-seq for the number of samples they wish to process. This will give an order number which can be used to reserve the Sandbox slot in the desired day and time in‘Genomics, Sandbox (room reservation)’.

TapeStation analysis

TapeStation on RNA or DNA samples is offered a service for Weizmann or external users. For further details please contact Muriel Chemla, muriel.chemla@weizmann.ac.il, Tel. 4435.

Blue Pippin

Consumables for Blue Pippin should be purchased directly from Zotal. If you are interested in using the Blue Pippin instrument , please order the instrument throgh the internal services - Bule Pippin. For further information contact Muriel Chemla, muriel.chemla@weizmann.ac.il, Tel. 4435

Sonication - Covaris

Consumables for Covaris should be purchased directly from Danyel Biotech. If you are interested in using the Covaris instrument , please order the instrument throgh the internal services - Sonication. For further information contact Muriel Chemla, muriel.chemla@weizmann.ac.il, Tel. 4435