{"text_format":"1","workbook":"xlsx","n_sheets":3,"sheets":["IMPORTANT NOTES","1. Guidelines","2. Sequencing Request 10X"],"not_rendered":{"charts":0,"images":3,"macros":0,"external_links":0,"defined_names":1,"comments":0,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1900"}

{"sheet":"IMPORTANT NOTES","index":0,"n_rows":20,"n_cols":2,"rows_kept":20,"cut":false,"hidden":false,"merged":[[1,1,1,15],[3,1,4,14],[5,1,7,14],[16,1,17,14],[14,1,15,14]]}
[]
[null,"IMPORTANT NOTES"]
[]
[null,"The CRG Genomics Unit is not responsible for the quality of samples provided by the user for single cell experiments. It is the user's responsibility to prepare them correctly and ensure that they are of the quality recommended by 10X Genomics."]
[]
[null,"Before performing a single cell experiment with 10X Genomics with a new cell type, the user must know how to properly prepare the cells or nuclei before providing them to the CRG Genomics Unit. To do so, he/she should contact Bonsai lab, Ana Borges, who will advise him/her on this matter (ana.borges@bonsailab.com)."]
[]
[]
[null,"Important aspects to be taken into account by the users (who prepares the cells or nuclei):"]
[null,"- Final result depends mainly on the quality of the sample (cells or nuclei). "]
[null,"- Before starting a new experiment the user must know how to handle the cells according to 10X Genomics quality standards. "]
[null,"- It is very important that cells are collected in PBS-0.04% BSA and nuclei in 1X Nuclei buffer (10X Genomics)*."]
[null,"- Related to the previous point, remember that It is very important NOT to resuspend the cells directly in water."]
[null,"- Use low binding tips and tubes. It is recommended use Rainin tips, but it can be used others, NEVER use (ART de Thermo, Bio-Rad, Denville y Axygen)."]
[null,"- Do NOT mix cells or nuclei with pipettes smaller than  P1000. To minimize physical damage to cells from shearing forces, it is critical to pipette gently and slowly during cell resuspensions."]
[]
[null,"- To recover the expected number of cells, it is critical to maximize viability, minimize the cell preparation time, accurately measure the input cell concentration and pipette the correct volume into each reaction."]
[]
[]
[null,"*Upon agreement on the day of the experiment, the CRG Genomics Unit will provide aliquots of 10X Nuclei buffer."]

{"sheet":"1. Guidelines","index":1,"n_rows":72,"n_cols":22,"rows_kept":72,"cut":false,"hidden":false,"merged":[[54,12,54,14],[9,1,9,18],[19,1,20,16],[25,1,25,2],[25,3,25,4],[25,5,25,9],[27,1,27,2],[27,3,27,4],[27,5,27,9],[28,1,28,2],[28,3,28,4],[28,5,28,9],[29,1,29,2],[29,3,29,4],[29,5,29,9],[32,1,33,17],[26,1,26,2],[26,3,26,4],[26,5,26,9],[42,1,43,16],[30,1,30,2],[30,3,30,4],[30,5,30,9]]}
[]
[null,"HOW TO FILL SEQUENCING REQUEST SAMPLES"]
[]
[null,"Remember that you have to fill 1 Request form per application. "]
[null,"* Mandatory fields"]
[]
[null,"CONTACT and SUBPROJECT DETAILS"]
["*","Main User: User responsible for the samples and the project. Please specify full name and contact e-mail."]
["*","PI name: PI responsible for the project. Please specify full name and contact e-mail."]
[null,"Additional contact 1 or 2: Any person that needs to receive information about the project and the final data. Please specify full name and contact e-mail."]
["*","Center: your institution."]
[null,"Group name: your group name inside your institution."]
[null,"Experiment name: name that you give to your experiment."]
[null,"Official code project: example FIS-089932."]
["*","CRG Quotation addressed to (name & email): Person to whom Genomics Unit have to address the quotation, usually PI or other collaborator who will pay the project."]
["*","CRG Quotation associated nº: CRG quotation number for the requested service. If you have not requested it in advance and you do not have it, please, leave it in blank."]
["*","TENDER / Minor contract reference: If the request are part of a TENDER or Minor Contract, please specify the reference. "]
[]
[null,"APPLICATION"]
["*","Application: Please, select the desired application. Multiome kit is out of Genomics Unit stock, so please contact Genomics Unit in advance. If you need other application not listed, please specify it in the corresponding field and contact Genomincs Unit."]
[]
[null,"SEQUENCING DETAILS"]
[null,"NEW - New sequencer available at the Genomics Unit, NEXTSEQ 2000."]
["*","Million reads / sample: nº of millions reads that you need for each sample."]
["*","Sequencing format: Please, indicate your desire sequencing format. Here you have a brief list of sequencer specifications:"]
[null,"Sequencer",null,"Flowcell / kit type",null,"Million reads per flowcell (Expected) "]
[null,"NovaSeq6000",null,"S2",null,3000]
[null,"NextSeq2000",null,"P2",null,400]
[null,"NextSeq2000",null,"P3",null,1200]
[null,"NextSeq500",null,"Mid Output",null,130]
[null,"NextSeq500",null,"High Output",null,400]
[]
[null,"Other length: If you need a run with a sequencing format not listed in the request, is mandatory to fill a complete run, take into account specifications for each sequencer. After that, please indicate the sequencing format (cycles for Read1 - index i7 - index i5 - Read2)."]
[]
[null,"In case of any doubts, contact Genomics Unit."]
["*","Not for sequencing: You only need library preparation, not sequencing at the Unit."]
[null,"Select one option: Sequencing format or Not for sequencing"]
[]
[null,"OBSERVATIONS"]
[null,"Please, indicate any important/special issue with your project."]
[]
[null,"SAMPLE DETAILS"]
["*","Sample Name: Use the same name as in the tube caps. Names should be alphanumerical, 6 characters maximum, no space, only accepted underscore. These fields have restrictions, in case of error it is indicated in the next columns, please correct it."]
[]
["*","Type of sample: Select just one option. For Gene Expression: cell suspension and for ATAC or Multiome: nuclei suspension."]
["*","Sample Specie: Use NCBI Taxonomy name, not taxonomy ID. Example: Homo sapiens, not 9606."]
[null,"Volume (ul): Please be sure that volume is correct for each sample."]
["*","Conc. (cells/ul or nuclei/ul): For Gene Expression cells/ul and for ATAC or Multiome nuclei/ul. Maximum 2 decimals."]
["*","Target Recovery: expected number of cells recovered and targeted."]
[null,"Low RNA content: Only for Gene Expression. Please, put yes or no, it gives us an idea how your cDNA and libraries will be."]
[null,"* These fields are mandatory for some parts of the protocol."]
[null,"If you paste values from other files, please PASTE AS VALUES"]
[null,"Once all information is correctly filled without errors, you can send Sequencing Request form to ngs@crg.eu."]
[]
[null,"Example how to fill Sequencing Request (10X Chromium)"]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Corrected names"]

{"sheet":"2. Sequencing Request 10X","index":2,"n_rows":177,"n_cols":48,"rows_kept":177,"cut":false,"hidden":false,"merged":[[73,35,73,40],[70,16,71,16],[21,4,21,6],[18,5,18,6],[19,5,19,6],[23,2,24,6],[23,8,24,14],[40,3,41,6],[72,2,72,13],[20,11,20,13],[8,11,8,13],[6,11,6,13],[22,11,22,13],[18,11,18,13],[12,11,12,13],[10,11,10,13],[16,11,16,13],[14,11,14,13],[6,4,6,6],[14,4,14,6],[10,5,10,6],[8,4,8,6],[12,5,12,6],[77,47,78,47],[76,43,77,43],[76,11,78,11],[76,6,78,6],[76,8,78,8],[76,7,78,7],[76,16,78,16],[76,10,78,10],[76,42,77,42],[76,35,77,40],[76,13,78,13],[76,32,78,32],[76,44,77,44],[76,12,78,12],[76,9,78,9],[76,3,78,3],[76,4,78,4],[76,5,78,5],[16,4,16,6],[60,2,64,13],[65,2,66,13],[70,2,71,13]]}
[]
[]
[null,null,"SEQUENCING REQUEST FORM (10X Chromium)",null,null,null,null,null,null,"GENOMICS UNIT - CRG Core Facilities"]
[]
[null,null,"CONTACT and SUBPROJECT DETAILS"]
[]
[null,null,"Main User Name:",null,null,null,null,null,null,"Main User contact e-mail: "]
[]
[null,null,"PI name:",null,null,null,null,null,null,"PI contact e-mail:"]
[]
[null,null,null,null,"Additional contact 1:",null,null,null,null,null,"Add. Contact 1 e-mail:"]
[]
[null,null,null,null,"Additional contact 2:",null,null,null,null,null,"Add. Contact 2 e-mail:"]
[]
[null,null,"Center: ",null,null,null,null,null,null,null,"Group Name:"]
[]
[null,null,"Experiment Name:",null,null,null,null,null,null,null,"Official code project:"]
[]
[null,null,"CRG Quotation adressed to (name):",null,null,null,null,null,null,null,"CRG Quotation associated nº:"]
[null,null,null,null,"(email):"]
[null,null,null,null,null,null,null,null,null,null,"TENDER / Minor contract reference:"]
[null,null,"Date:"]
[null,null,null,null,null,null,null,null,null,null,"CRG subproject nº:"]
[null,null,"APPLICATION & PROTOCOL & 10X recommended sequencing formats",null,null,null,null,null,"SEQUENCING FORMAT "]
[]
[]
[null,null,null,"Gene Expression - Next GEM Single Cell 3ʹ Reagent Kits v3.1",null,null,null,null,"Million reads / sample:"]
[null,null,null,"Minimum read pairs per cell: 20,000"]
[null,null,null,"Read 1:","28 cycles",null,null,null,"NovaSeq6000 - NEW"]
[null,null,null,"i7 Index:","10 cycles",null,null,null,"Format",null,null,"Flowcell"]
[null,null,null,"i5 Index:","10 cycles",null,null,null,null,"2 x 50    (paired end - 50bp)",null,null,"S2"]
[null,null,null,"Read 2:","91 cycles",null,null,null,null,"2 x 150  (paired end - 150bp)"]
[null,null,null,null,null,null,null,null,"For other run formats and flowcells types, please contact Genomics Unit."]
[null,null,null,"ATACseq -  Next GEM Single Cell ATAC Reagent Kits v1.1"]
[null,null,null,"Minimum read pairs per nucleus: 25,000",null,null,null,null,"NextSeq2000"]
[null,null,null,"Read 1:","50 cycles",null,null,null,"Format",null,null,"Flowcell",null,"Cycles kit"]
[null,null,null,"i7 Index:","8 cycles",null,null,null,null,"1 x 50    (single read - 50bp)",null,null,"P2",null,50]
[null,null,null,"i5 Index:","16 cycles",null,null,null,null,"2 x 50    (paired end - 50bp)",null,null,"P3",null,100]
[null,null,null,"Read 2:","50 cycles",null,null,null,null,"2 x 100  (paired end - 100bp)",null,null,null,null,200]
[null,null,null,null,null,null,null,null,null,"2 x 150  (paired end - 150bp)",null,null,null,null,300]
[null,null,null,"Multiome - Next GEM Single Cell Multiome ATAC + Gene Expression.                     We do not have the kit in stock, so please contact Genomics Unit in advance.",null,null,null,null,null,"Other length*"]
[]
[null,null,null,"Gene Expression",null,null,null,null,"NextSeq500"]
[null,null,null,"Minimum read pairs per cell: 20,000",null,null,null,null,"Format",null,null,"Flowcell",null,"Cycles kit"]
[null,null,null,"Read 1:","28 cycles",null,null,null,null,"1 x 75    (single read - 75bp)",null,null,"MID output",null,75]
[null,null,null,"i7 Index:","10 cycles",null,null,null,null,"2 x 75    (paired end - 75bp)",null,null,"HIGH output",null,150]
[null,null,null,"i5 Index:","10 cycles",null,null,null,null,"2 x 150  (paired end - 150bp)",null,null,null,null,300]
[null,null,null,"Read 2:","91 cycles",null,null,null,null,"Other length*"]
[]
[null,null,null,"ATAC",null,null,null,null,"*Other length: you will fill a complete run. Please, specify sequencing format:"]
[null,null,null,"Minimum read pairs per nucleus: 25,000",null,null,null,null,null,"Read 1","index i7","index i5","Read 2"]
[null,null,null,"Read 1:","50 cycles",null,null,null,"Cycles"]
[null,null,null,"i7 Index:","8 cycles"]
[null,null,null,"i5 Index:","24 cycles",null,null,null,null,"Not for sequencing"]
[null,null,null,"Read 2:","49 cycles"]
[]
[null,null,null,"Other application/protocol/sequencing format: please, contact Genomincs Unit"]
[]
[null,null,"OBSERVATIONS"]
[]
[]
[]
[]
[]
[]
[null,null,"IMPORTANT: Samples, libraries and sequencing data will be kept for 6 months  after service has been completed.  After that, samples and libraries will be discarded if user have not pick them up, and data will be deleted."]
[]
[]
[null,null,"SAMPLE DETAILS:"]
[]
[null,null,"IMPORTANT: Please read carefully \"Guidelines\" tab to fill correctly the required information.  ",null,null,null,null,null,null,null,null,null,null,null,null,null,"TYPE OF ERRORS"]
[]
[null,null,"Names should be alphanumerical, 6 characters maximum, no space, only accepted underscore.",null,null,null,null,null,null,null,null,null,null,null,null,null,"Duplicate names"]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Plate Name separado"]
[null,null,null,"NOTE: If you want to copy values from other file, PASTE AS VALUES",null,null,null,null,null,null,null,null,null,null,null,null,"More than 6 characters or not accepted character used"]
[]
[null,null,null,"CRG SAMPLE Barcode         (filled by Genomics Unit)","Sample Name                (6 characters,no space, only underscore)","Type of sample     (cell suspension, nuclei suspension)","Sample Specie Name                  (Use NCBI Taxonomy)","Volume       (ul)","Concentration (cells/ul or nuclei/ul)","Target recovery","Low RNA content       (only for scGE)","Observations","Sample Condition","Sample   Replicate",null,null,"Sample Name Error, please correct it",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"well plate (just in case plate filled)",null,null,"Sample Name separado",null,null,null,null,null,null,"Concatenado (incluye\"error\")","encuentra \"error\" y te da la 1º posicion","Comment \"error\" at 1st position"]
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[]
[null,null,null,"NOTE: If you have more than 96 samples, please fill new request form for next samples."]