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["TREX Sample Submission"]
["Instructions and important notes",null,null,null,null,"Version 1.0"]
["1. Please complete this form electronically with detailed and accurate information. Fields marked with an asterisk (*) are required. Shaded areas are for TREX staff only; please do not edit/change."]
["2. Please send an electronic copy (Excel format) to TREX (trex_info@cornell.edu) BEFORE you submit your samples."]
["3. Please send samples in 1.5 ml microcentrifuge tubes. Incorrect tubes risk delays and handling fees."]
["4. When labeling bags or boxes for holding tubes please do NOT use Tape as it often comes off at -80. "]
[]
["For TREX use ONLY","Project ID #",null,null,null,"Submission Date",null,"Date Received",null,null,"QC Complete"]
["Project Information","Project Name*",null,null,null,"Primary Contact","Name*",null,null,null,"Initials*",{"$f":"LEFT($H$9)&IF(ISNUMBER(FIND(\" \",$H$9)),MID($H$9,FIND(\" \",$H$9)+1,1),\"\")&IF(ISNUMBER(FIND(\" \",$H$9,FIND(\" \",$H$9)+1)),MID($H$9,FIND(\" \",$H$9,FIND(\" \",$H$9)+1)+1,1),\"\")","v":""}]
[null,"Payment Method (Cornell Account)*",null,null,null,null,"e-mail*"]
["PI Information","PI Name*",null,null,null,"Department*"]
[null,"PI E-mail*",null,null,null,"Would you like your sample returned? *","Yes/No"]
[]
["RNA information*\n\nPlease answer each question separately; every field is required","Number of samples (# of tubes) ",null,null,null,"Library Type: select from the drop down menu below",null,null,"RNA enrichment method: select from the drop down menu below"]
[null,"Species",null,null,null,"Use this drop down menu to select library type *",null,null,"Use this drop down menu to select RNA enrichment method *"]
[null,"*Human Samples require Confidentiality Agreement*"]
[null,"RNA Quantification done",null,null,"Yes/No/NA"]
[null,"If RNA samples have been quantified, what instrument did you use? If RNA samples have not been quantified please include details in the notes.",null,null,"Use this drop down menu to select quantification instrument","Project Notes:"]
[null,"RNA Integrity Quality Check done",null,null,"Yes/No/NA"]
[null,"If RNA integrity was checked, what instrument did you use?",null,null,"Use this drop down menu to select quality check instrument"]
[]
["How much total total RNA should I send?","Library Type",null,null,"Stranded RNAseq",null,"Non-Stranded RNAseq",null,null,"Small RNA seq"]
[null,"Strongly recommended",null,null,"At least 15uL with total input of 2000 ng",null,"Use Stranded RNA Seq",null,null,"At least 15uL with total input >500ng"]
[null,"Required\nMust also pass other quality control tests",null,null,"At least 15uL with total input of 20ng",null,"At least 15uL with total input lower than 20ng",null,null,"At least 15uL with total input of 100ng"]
[]
["Sequencing ","Read Length","Standard: 75bp SE reads",null,"Our Standard sequencing length is 75bp SE reads, if you would like a read length OTHER than 75bp SE you are required to use the whole flowcell.",null,null,null,"Read Length",null,"Use this drop down menu to select Read Length"]
[null,"Read Depth","Standard:                                          RNASeq: 20 Million reads/sample                                  SmallRNA: 10 Million reads/sample",null,"Our Standard sequencing depth is 20 million reads/sample for RNA-Seq, 10 million reads/sample for smRNA-Seq. If you would like additional read depth we provide additional depth in 10 or 20 million read increments.",null,null,null,"Read Depth",null,"Use this drop down menu to select Read Depth"]
[]
["Analysis","Reference (The default will be the most up to date version for your species at Ensembl. If you have a specific assembly or annotation your prefer, please specify it here)",null,null,null,null,null,null,"Default (unless changed here)"]
[null,"Select Tier for Analysis","We offer 4 tiers of analysis, as detailed below, please select which tier you would prefer from the drop down menu provided",null,null,null,null,null,"*Use this drop down menu to select which Tier of Analysis you would like"]
[null,null,"1. Tier I (Base): Data QC and Mapping only. Distribution of QC report, raw counts table, and FASTQ on request."]
[null,null,"2. Tier II (Gene Expression Analysis): Base + test/s for differential expression for annotated genes. For this tier it is necessary to submit biological replicates for all conditions and to provide detailed information in the \"contrast\" section of the sample submission table below. "]
[null,null,"3. Tier III (Pathogen ID): Base + split fastq files into host and non-host reads. "]
[null,null,"4. Custom: Must consult with the Director BEFORE submission. Provide details of consultation in the \"Project Notes\" section."]
[]
["Important Instructions for Sample Information"]
["1.","Sample and Group names need to be ≤ 20 characters and can use letter, number and dash ONLY (NO Spaces or underscores). "]
["2.","If you have checked your RNA quality (Fragment Analyzer/BioAnalyzer/Tapestation) or quantity (Qubit/Nanodrop), please email a copy of any results along with your submission form"]
["3.","Sample tubes should be labeled with black Sharpie on both the lid AND side of the tube with the Library Name or Sample Name."]
["4.","For data analysis, please define all groups/treatments/replicates. Refer to the example Sample Information template for further information"]
[]
["Sample Information*","Library Name (Initials, #) - AUTOFILL","* Sample Name (Designated by customer)",null,"RQN (If this section is left blank please comment why in \"remarks\")","RNA Concentration (ng/uL)","Volume (please submit at least 15uL)","Group/Replicate ID: (insert group name here) Example: Timepoint",null,"Group 2/ Replicate ID: (insert group name here) Example: drug treatment",null,"Remarks (as appropriate)","ERROR CODE","ERROR TYPE"]
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[{"$f":"IF(ROW(A44)-42<=$E$14,ROW(A44)-42,\"\")","v":""},{"$f":"IF(A44=\"\",\"\",'sample table mirror'!A4)","v":""},null,null,null,null,null,null,null,null,null,null,{"$f":"'sample table mirror'!L4","v":0},{"$f":"IF(M44>0,IF(M44<10,\"Sample Name can have letters, numbers, and dash (-) only. No spaces or other characters please!\",IF(M44=10,\"Sample Names must be unique!\",IF(M44=100,\"Sample count above doesn’t match sample list!\"))),\"\")","v":""}]
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["",{"$f":"IF(A186=\"\",\"\",'sample table mirror'!A146)","v":""},null,null,null,null,null,null,null,null,null,null,{"$f":"'sample table mirror'!L146","v":0},""]
["",{"$f":"IF(A187=\"\",\"\",'sample table mirror'!A147)","v":""},null,null,null,null,null,null,null,null,null,null,{"$f":"'sample table mirror'!L147","v":0},""]
["",{"$f":"IF(A188=\"\",\"\",'sample table mirror'!A148)","v":""},null,null,null,null,null,null,null,null,null,null,{"$f":"'sample table mirror'!L148","v":0},""]
["",{"$f":"IF(A189=\"\",\"\",'sample table mirror'!A149)","v":""},null,null,null,null,null,null,null,null,null,null,{"$f":"'sample table mirror'!L149","v":0},""]
["",{"$f":"IF(A190=\"\",\"\",'sample table mirror'!A150)","v":""},null,null,null,null,null,null,null,null,null,null,{"$f":"'sample table mirror'!L150","v":0},""]
["",{"$f":"IF(A191=\"\",\"\",'sample table mirror'!A151)","v":""},null,null,null,null,null,null,null,null,null,null,{"$f":"'sample table mirror'!L151","v":0},""]
["",{"$f":"IF(A192=\"\",\"\",'sample table mirror'!A152)","v":""},null,null,null,null,null,null,null,null,null,null,{"$f":"'sample table mirror'!L152","v":0},""]
["end","end","end","end","end","end","end","end","end","end","end","end","end","end"]
[]
["If you have more than 150 samples, please contact trex_info@cornell.edu"]

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["TREX Sample Submission"]
["Instructions and important notes",null,null,null,null,"Version 1.0"]
["1. Please complete this form electronically with detailed and accurate information. Fields marked with an asterisk (*) are required. Shaded areas are for TREX staff only; please do not edit/change."]
["2. Please send an electronic copy (Excel format) to TREX (trex_info@cornell.edu) BEFORE you submit your samples."]
["3. Please send samples in 1.5 ml microcentrifuge tubes. Incorrect tubes risk delays and handling fees."]
["4. When labeling bags or boxes for holding tubes please do NOT use Tape as it often comes off at -80. "]
[]
["For TREX use ONLY","Project ID #",null,null,null,"Submission Date",null,"Date Received",null,null,"QC Complete"]
["Project Information","Project Name*","My Research Topic",null,null,"Primary Contact","Name*","Jane Doe",null,null,"Initials*",{"$f":"LEFT($H$9)&IF(ISNUMBER(FIND(\" \",$H$9)),MID($H$9,FIND(\" \",$H$9)+1,1),\"\")&IF(ISNUMBER(FIND(\" \",$H$9,FIND(\" \",$H$9)+1)),MID($H$9,FIND(\" \",$H$9,FIND(\" \",$H$9)+1)+1,1),\"\")","v":"JD"}]
[null,"Payment Method (Cornell Account)*","101-0101",null,null,null,"e-mail*","jd01@cornell.edu"]
["PI Information","PI Name*","My PI",null,null,"Department*","My Home"]
[null,"PI E-mail*","pi01@cornell.edu",null,null,"Would you like your sample returned? *","No-We will discard the samples once sequencing is complete"]
[]
["RNA information*\n\nPlease answer each question separately; every field is required","Number of samples (# of tubes) ",null,null,12,"Library Type: select from the drop down menu below",null,null,"RNA enrichment method: select from the drop down menu below"]
[null,"Species",null,null,"Mouse","RNAseq - Stranded (default)",null,null,"Poly A"]
[null,"*Human Samples require Confidentiality Agreement*"]
[null,"RNA Quantification done",null,null,"Yes"]
[null,"If RNA samples have been quantified, what instrument did you use? If RNA samples have not been quantified please include details in the notes.",null,null,"Nanodrop (please provide data)","Project Notes:"]
[null,"RNA Integrity Quality Check done",null,null,"Yes"]
[null,"If RNA integrity was checked, what instrument did you use?",null,null,"Fragment Analyzer"]
[]
["How much total total RNA should I send?","Library Type",null,null,"Stranded RNAseq",null,"Non-Stranded RNAseq",null,null,"Small RNA seq"]
[null,"Strongly recommended",null,null,"At least 15uL with total input of 2000 ng",null,"Use Stranded RNA Seq",null,null,"At least 15uL with total input >500ng"]
[null,"Required\nMust also pass other quality control tests",null,null,"At least 15uL with total input of 20ng",null,"At least 15uL with total input lower than 20ng",null,null,"At least 15uL with total input of 100ng"]
[]
["Sequencing ","Read Length","Standard: 75bp SE reads",null,"Our Standard sequencing length is 75bp SE reads, if you would like a read length OTHER than 75bp SE you are required to use the whole flowcell.",null,null,null,"Read Length",null,"Standard - 75nt SE"]
[null,"Read Depth","Standard:                                          RNASeq: 20 Million reads/sample                                  SmallRNA: 10 Million reads/sample",null,"Our Standard sequencing depth is 20 million reads/sample for RNA-Seq, 10 million reads/sample for smRNA-Seq. If you would like additional read depth we provide additional depth in 10 or 20 million read increments.",null,null,null,"Read Depth",null,"20M reads/sample (standard RNAseq)"]
[]
["Analysis","Reference (The default will be the most up to date version of your species in Ensembl, if you have a specific assembly or annotation your prefer, please specify it here)",null,null,null,null,null,null,"*Reference Genome"]
[null,"Select Tier for Analysis","We offer 4 tiers of analysis, as detailed below, please select which tier you would prefer from the drop down menu provided",null,null,null,null,null,"*Use this drop down menu to select which Tier of Analysis you would like"]
[null,null,"1. Tier I (Base): Data QC and Mapping only. Distribution of QC report, raw counts table, and FASTQ on request."]
[null,null,"2. Tier II (Gene Expression Analysis): Base + test/s for differential expression for annotated genes. For this tier it is necessary to submit biological replicates for all conditions and to provide detailed information in the \"contrast\" section of the sample submission table below. "]
[null,null,"3. Tier III (Pathogen ID): Base + split fastq files into host and non-host reads. "]
[null,null,"4. Custom: Must consult with the Director BEFORE submission. Provide details of consultation in the \"Project Notes\" section."]
[]
["Important Instructions for Sample Information"]
["1.","Sample and Group names need to be ≤ 20 characters and can use letter, number and dash ONLY (NO Spaces or underscores). "]
["2.","If you have checked your RNA quality (Fragment Analyzer/BioAnalyzer/Tapestation) or quantity (Qubit/Nanodrop), please email a copy of any results along with your submission form"]
["3.","Sample tubes should be labeled with black Sharpie on both the lid AND side of the tube with the Library Name or Sample Name."]
["4.","For data analysis, please define all groups/treatments/replicates. Refer to the example Sample Information template for further information"]
[]
["Sample Information*","Library Name (Initials, #) - AUTOFILL","* Sample Name (Designated by customer)",null,"RQN (If this section is left blank please comment why in \"remarks\")","RNA Concentration (ng/uL)","Volume (please submit at least 15uL)","Group/Replicate ID: (insert group name here) Example: Timepoint",null,"Group 2/ Replicate ID: (insert group name here) Example: drug treatment",null,"Remarks (as appropriate)","ERROR CODE","ERROR TYPE"]
[{"$f":"IF(ROW(A43)-42<=$E$14,ROW(A43)-42,\"\")","v":1},"JD1","T0-R1",null,8.3000000000000007,100,15,"Pre",null,null,null,null,0,{"$f":"IF(M43>0,IF(M43<10,\"Sample Name can have letters, numbers, and dash (-) only. No spaces or other characters please!\",\"Sample Names must be unique!\"),\"\")","v":""}]
[{"$f":"IF(ROW(A44)-42<=$E$14,ROW(A44)-42,\"\")","v":2},"JD2","T0-R2",null,8.5,100,15,"Pre",null,null,null,null,0,{"$f":"IF(M44>0,IF(M44<10,\"Sample Name can have letters, numbers, and dash (-) only. No spaces or other characters please!\",\"Sample Names must be unique!\"),\"\")","v":""}]
[3,"JD3","T0-R3",null,9,100,15,"Pre",null,null,null,null,0,""]
[4,"JD4","Vehicle-T24-R1",null,8.4,100,15,"Vehicle",null,null,null,null,0,""]
[5,"JD5","Vehicle-T24-R2",null,7.8,100,15,"Vehicle",null,null,null,null,0,""]
[6,"JD6","Vehicle-T24-R3",null,9,100,15,"Vehicle",null,null,null,null,0,""]
[7,"JD7","DrugLowDose-T24-R1",null,9.3000000000000007,100,15,"Low",null,null,null,null,0,""]
[8,"JD8","DrugLowDose-T24-R2",null,8.1999999999999993,100,15,"Low",null,null,null,null,0,""]
[9,"JD9","DrugLowDose-T24-R3",null,8.5,100,15,"Low",null,null,null,null,0,""]
[10,"JD10","DrugHighDose-T24-R1",null,9.1,100,15,"High",null,null,null,null,0,""]
[11,"JD11","DrugHighDose-T24-R2",null,8.6999999999999993,100,15,"High",null,null,null,null,0,""]
[12,"JD12","DrugHighDose-T24-R3",null,7.8,100,15,"High",null,null,null,null,0,""]
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[]
["If you have more than 150 samples, please contact trex_info@cornell.edu"]

{"sheet":"Source code","index":2,"n_rows":32,"n_cols":6,"rows_kept":32,"cut":false,"hidden":true,"merged":[]}
[]
[]
["Use this drop down menu to select quantification instrument","Use this drop down menu to select RNA enrichment method *",null,"Use this drop down menu to select library type *",null,"Use this drop down menu to select desired data output"]
["Qubit (or other intercalating dye system)","Poly A",null,"RNAseq - Stranded (default)",null,"Full HiSeq lane (110G)"]
["Nanodrop (please provide data)","Ribosomal Depletion: Human/Rat/Mouse (for animal samples)",null,"RNAseq - non stranded (low input)",null,"Equally shared HiSeq lane (≥2 libraries assigned to a particular lane)"]
["Other (Please describe in \"Notes\")","Ribosomal Depletion: Bacterial",null,"small RNA",null,"Unequally shared HiSeq lane (please give details in notes)"]
["None (Please describe why in \"Notes\")","Ribosomal Depletion: Plant  (must provide depletion kit)",null,null,null,"Full NovaSeq S2 flowcell (1T)"]
[null,"None",null,null,null,"Equally shared NovaSeq S2 flowcell (≥2 libraries assigned to a particular lane)"]
[null,"Cell Free RNA",null,null,null,"Unequally shared NovaSeq S2 flowcell (please give details in \"remarks\")"]
[null,"Other (Please clarify in \"Notes\")",null,null,null,"Full NovaSeq S4 lane (800G)"]
["Use this drop down menu to select quality check instrument","*Use this drop down menu to select which Tier of Analysis you would like",null,null,null,"Equally shared NovaSeq S4 lane (≥2 libraries assigned to a particular lane)"]
["Fragment Analyzer","Tier I: Base",null,null,null,"Unequally shared NovaSeq S4 lane (please give details in \"remarks\")"]
["BioAnalyzer","Tier II: Gene Expression",null,"Technical support use only",null,"Full NovaSeq S4 flowcell (3.2T, four lanes)"]
["Tapestation ","Tier III: Pathogen Identification",null,"PCR-free library",null,"Other (please describe in notes)"]
["Gel","Custom: Must consult with director PRIOR to project submission",null,"10X Genomics RNA library"]
["Other (Please describe in \"Notes\")",null,null,"10X Genomics DNA library"]
["None (Please describe why in \"Notes\")",null,null,"Low diversity library"]
[null,null,null,"Unbalanced library"]
[null,"Yes - We will return any remaining sample to you once sequencing is complete",null,"Needs dilution"]
[null,"No-We will discard the samples once sequencing is complete",null,"Needs sample tube combination"]
["Use this drop down menu to select Read Length",null,null,"Custom primer"]
["Standard - 75nt SE",null,null,"Originally FFPE or other embedded sample"]
["Custom - dedicated flowcell (Please describe in \"Notes\")","Yes",null,"Custom insert size"]
[null,"No - Please describe why in \"Notes\" field",null,"Had globin removal"]
[null,"NA- Please describe why in \"Notes\" field",null,"Unusual data amount"]
[null,null,null,"PDX or infection/symbiosis"]
[null,null,null,"Other (please type it in)"]
[]
["Use this drop down menu to select Read Depth"]
["20M reads/sample (standard RNAseq)"]
["10M reads/sample (standard small RNA or bacterial RNAseq)"]
["Custom read depth: include details in notes"]

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