title: T1R2_TMD Dimer_Sorted Library; replicate 1

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description: Deep mutaional scan for dimerization with T1R3

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script: ECD1 Fragment A read 1: python2.7 Paired_read_fuser.py --path express1_fragA_R1/ --read1 T1R2_ECD1_express1_R1.fastq.bz2 --read2 T1R2_ECD1_express1_R1.fastq.bz2 --wtseq GCTGAGAACTCGGACTTCTACCTGCCTGGGGATTACCTCCTGGGTGGCCTCTTCTCCCTCCATGCCAACATGAAGGGCATTGTTCACCTTAACTTCCTGCAGGTGCCCATGTGCAAGGAGTATGAAGTGAAGGTGATAGGCTACAACCTCATGCAGGCCATGCGCTTTGCGGTGGAGGAGATCAACAATGACAGCAGCCTGCTGCCTGGT --read1_overlap_start 38 --read1_overlap_end 248 --mode R1
Fuser script: ECD1 Fragment A read 2: python2.7 Paired_read_fuser.py --path express1_fragA_R2/ --read1 T1R2_ECD1_express1_R2.fastq.bz2 --read2 T1R2_ECD1_express1_R2.fastq.bz2 --wtseq GTGGCCAACTTCCTCTCCCTATTTCTCCTTCCACAGATCACCTACAGCGCCATCAGCGATGAGCTGCGAGACAAGGTGCGCTTCCCGGCTTTGCTGCGTACCACACCCAGCGCCGACCACCACATCGAGGCCATGGTGCAGCTTATGCTGCACTTCCGCTGGAACTGGATCATTGTGCTGGTGAGCAGCGACACCTATGGCCGC --read2_overlap_start 27 --read2_overlap_end 231 --mode R2
Fuser script: ECD1 Fragment B read 1: python2.7 Paired_read_fuser.py --path express1_fragB_R1/ --read1 T1R2_ECD1_express1_R1.fastq.bz2 --read2 T1R2_ECD1_express1_R1.fastq.bz2 --wtseq AGCAGCCTGCTGCCTGGTGTGCTGCTGGGCTATGAGATCGTGGATGTGTGCTACATCTCCAACAATGTCCAGCCGGTGCTCTACTTCCTGGCACACGAGGACAACCTCCTTCCCATCCAAGAGGACTACAGTAACTACATTTCCCGTGTGGTGGCTGTCATTGGCCCTGACAACTCCGAGTCTGTCATGACTGTGGCCAACTTCCTCTCCCTATTTCTCCTTCCACAG --read1_overlap_start 22 --read1_overlap_end 250 --mode R1
Fuser script: ECD1 Fragment B read 2: python2.7 Paired_read_fuser.py --path express1_fragB_R2/ --read1 T1R2_ECD1_express1_R2.fastq.bz2 --read2 T1R2_ECD1_express1_R2.fastq.bz2 --wtseq GACAATGGCCAGCTGCTTGGCGAGCGCGTGGCCCGGCGCGACATCTGCATCGCCTTCCAGGAGACGCTGCCCACACTGCAGCCCAACCAGAACATGACGTCAGAGGAGCGCCAGCGCCTGGTGACCATTGTGGACAAGCTtCAGCAGAGCACAGCGCGCGTCGTGGTCGTGTTCTCGCCCGACCTGACCCTGTACCACTTCTTC --read2_overlap_start 19 --read2_overlap_end 223 --mode R2
Fuser script: ECD2 Fragment A read 1: python2.7 Paired_read_fuser.py --path express1_fragA_R1/ --read1 T1R2_ECD2_express1_R1.fastq.bz2 --read2 T1R2_ECD2_express1_R1.fastq.bz2 --wtseq AATGAGGTGCTGCGCCAGAACTTCACTGGCGCCGTGTGGATCGCCTCCGAGTCCTGGGCCATCGACCCGGTCCTGCACAACCTCACGGAGCTGCGCCACTTGGGCACCTTCCTGGGCATCACCATCCAGAGCGTGCCCATCCCGGGCTTCAGTGAGTTCCGCGAGTGGGGCCCACAGGCTGGGCCGCCACCCCTCAGCAGGACCAGCCAGAGCTATACCTGCAACCAGGAG --read1_overlap_start 19 --read1_overlap_end 250 --mode R1
Fuser script: ECD2 Fragment A read 2: python2.7 Paired_read_fuser.py --path express1_fragA_R2/ --read1 T1R2_ECD2_express1_R2.fastq.bz2 --read2 T1R2_ECD2_express1_R2.fastq.bz2 --wtseq TACCCCTGGCAGCTGCTcGAGGAGATCTGGAAGGTCAACTTCACTCTCCTGGACCACCAAATCTTCTTCGACCCGCAAGGGGACGTGGCTCTGCACTTGGAGATTGTCCAGTGGCAATGGGACCGGAGCCAGAATCCCTTCCAGAGCGTCGCCTCCTACTACCCCCTGCAGCGACAGCTGAAGAACATCCAAGACATCTCC --read2_overlap_start 29 --read2_overlap_end 230 --mode R2
Fuser script: ECD2 Fragment B read 1: python2.7 Paired_read_fuser.py --path express1_fragB_R1/ --read1 T1R2_ECD2_express1_R1.fastq.bz2 --read2 T1R2_ECD2_express1_R1.fastq.bz2 --wtseq TGCAACCAGGAGTGCGACAACTGCCTGAACGCCACCTTGTCCTTCAACACCATTCTCAGGCTCTCTGGGGAGCGTGTCGTCTACAGCGTGTACTCTGCGGTCTATGCTGTGGCCCATGCCCTGCACAGCCTCCTCGGCTGTGACAAAAGCACCTGCACCAAGAGGGTGGTCTACCCCTGGCAGCTGCTcGAGGAGATCTGGAAGGTCAACTTCACTCTCCTGGACCAC --read1_overlap_start 21 --read1_overlap_end 249 --mode R1
Fuser script: ECD2 Fragment B read 2: python2.7 Paired_read_fuser.py --path express1_fragB_R2/ --read1 T1R2_ECD2_express1_R2.fastq.bz2 --read2 T1R2_ECD2_express1_R2.fastq.bz2 --wtseq TGGCACACCATCAACAACACGATCCCTATGTCCATGTGTTCCAAGAGGTGCCAGTCAGGGCAAAAGAAGAAGCCTGTGGGCATCCACGTCTGCTGCTTCGAGTGCATCGACTGCCTTCCCGGCACCTTCCTCAACCACACTGAAGATGAATATGAATGCCAGGCCTGCCCGAATAACGAGTGGTCCTACCAGAGTGAGACC --read2_overlap_start 23 --read2_overlap_end 224 --mode R2
Fuser script: TMD Fragment A read 1: python2.7 Paired_read_fuser.py --path express1_fragA_R1/ --read1 T1R2_TMD_express1_R1.fastq.bz2 --read2 T1R2_TMD_express1_R1.fastq.bz2 --wtseq TCCTGCTTCAAGCGGCAGCTGGTCTTCCTGGAATGGCATGAGGCACCCACCATCGCTGTGGCCCTGCTGGCCGCCCTGGGCTTCCTCAGCACCCTGGCCATCCTGGTGATATTCTGGAGGCACTTCCAGACACCCATcGTaCGCTCGGCTGGGGGCCCCATGTGCTTCCTGATGCTGACACTGCTGCTGGTGGCATACATGGTGGTC --read1_overlap_start 31 --read1_overlap_end 238 --mode R1
Fuser script: TMD Fragment A read 2: python2.7 Paired_read_fuser.py --path express1_fragA_R2/ --read1 T1R2_TMD_express1_R2.fastq.bz2 --read2 T1R2_TMD_express1_R2.fastq.bz2 --wtseq TTCCAGATCGTCTGCGCCTTCAAGATGGCCAGCCGCTTCCCACGCGCCTACAGCTACTGGGTCCGCTACCAGGGGCCCTACGTCTCTATGGCATTTATCACGGTACTCAAAATGGTCATTGTGGTAATTGGCATGCTGGCCACGGGCCTCAGTCCCACCACCCGTACTGACCCCGATGACCCCAAGATCACAATTGTCTCCTGTAATCCCAACTACCGC --read2_overlap_start 11 --read2_overlap_end 230 --mode R2
Fuser script: TMD Fragment B read 1: python2.7 Paired_read_fuser.py --path express1_fragB_R1/ --read1 T1R2_TMD_express1_R1.fastq.bz2 --read2 T1R2_TMD_express1_R1.fastq.bz2 --wtseq CTGCTGCTGGTGGCATACATGGTGGTCCCGGTGTACGTGGGGCCGCCCAAGGTCTCCACCTGCCTCTGCCGCCAGGCCCTCTTTCCCCTCTGCTTCACAATCTGCATCTCCTGTATCGCCGTGCGTTCTTTCCAGATCGTCTGCGCCTTCAAGATGGCCAGCCGCTTCCCACGCGCCTACAGCTACTGGGTCCGCTACCAGGGGCCCTACGTCTCTATG --read1_overlap_start 21 --read1_overlap_end 240 --mode R1
Fuser script: TMD Fragment B read 2: python2.7 Paired_read_fuser.py --path express1_fragB_R2/ --read1 T1R2_TMD_express1_R2.fastq.bz2 --read2 T1R2_TMD_express1_R2.fastq.bz2 --wtseq TGTAATCCCAACTACCGCAACAGCCTGCTGTTCAACACCAGCCTGGACCTGCTGCTCTCAGTGGTGGGTTTCAGCTTCGCCTACATGGGCAAAGAGCTGCCCACCAACTACAACGAGGCCAAGTTCATCACCCTCAGCATGACCTTCTATTTCACCTCATCCGTCTCCCTCTGCACCTTCATGTCTGCCTACAGCGGGGTGCTGGTCACCATCGTGGAC --read2_overlap_start 12 --read2_overlap_end 231 --mode R2
Fuser script: TMD Fragment C read 1: python2.7 Paired_read_fuser.py --path express1_fragC_R1/ --read1 T1R2_TMD_express1_R1.fastq.bz2 --read2 T1R2_TMD_express1_R1.fastq.bz2 --wtseq GCCAGCCGCTTCCCACGCGCCTACAGCTACTGGGTCCGCTACCAGGGGCCCTACGTCTCTATGGCATTTATCACGGTACTCAAAATGGTCATTGTGGTAATTGGCATGCTGGCCACGGGCCTCAGTCCCACCACCCGTACTGACCCCGATGACCCCAAGATCACAATTGTCTCCTGTAATCCCAACTACCGCAACAGCCTGCTGTTCAACACCAGCCTG --read1_overlap_start 21 --read1_overlap_end 240 --mode R1
Fuser script: TMD Fragment C read 2: python2.7 Paired_read_fuser.py --path express1_fragC_R2/ --read1 T1R2_TMD_express1_R2.fastq.bz2 --read2 T1R2_TMD_express1_R2.fastq.bz2 --wtseq GTCTCCCTCTGCACCTTCATGTCTGCCTACAGCGGGGTGCTGGTCACCATCGTGGACCTCTTGGTCACTGTGCTCAACCTCCTGGCCATCAGCCTGGGCTACTTCGGCCCCAAGTGCTACATGATCCTCTTCTACCCGGAGCGCAACACGCCCGCCTACTTCAACAGCATGATCCAGGGCTACACCATG --read2_overlap_start 13 --read2_overlap_end 202 --mode R2
Aligner script: ECD1 Fragment A read 1: python2.7 Fused_read_aligner.py --path express1_fragA_R1/ --infile T1R2_ECD1_express1_R1.fast_R1_qc1 --referenceDNA GCTGAGAACTCGGACTTCTACCTGCCTGGGGATTACCTCCTGGGTGGCCTCTTCTCCCTCCATGCCAACATGAAGGGCATTGTTCACCTTAACTTCCTGCAGGTGCCCATGTGCAAGGAGTATGAAGTGAAGGTGATAGGCTACAACCTCATGCAGGCCATGCGCTTTGCGGTGGAGGAGATCAACAATGACAGCAGCCTGCTGCCTGGT --referenceAA AENSDFYLPGDYLLGGLFSLHANMKGIVHLNFLQVPMCKEYEVKVIGYNLMQAMRFAVEEINNDSSLLPG --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: ECD1 Fragment A read 2: python2.7 Fused_read_aligner.py --path express1_fragA_R2/ --infile T1R2_ECD1_express1_R2.fast_R2_qc1 --referenceDNA GTGGCCAACTTCCTCTCCCTATTTCTCCTTCCACAGATCACCTACAGCGCCATCAGCGATGAGCTGCGAGACAAGGTGCGCTTCCCGGCTTTGCTGCGTACCACACCCAGCGCCGACCACCACATCGAGGCCATGGTGCAGCTTATGCTGCACTTCCGCTGGAACTGGATCATTGTGCTGGTGAGCAGCGACACCTATGGCCGC --referenceAA VANFLSLFLLPQITYSAISDELRDKVRFPALLRTTPSADHHIEAMVQLMLHFRWNWIIVLVSSDTYGR --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: ECD1 Fragment B read 1: python2.7 Fused_read_aligner.py --path express1_fragB_R1/ --infile T1R2_ECD1_express1_R1.fast_R1_qc1 --referenceDNA AGCAGCCTGCTGCCTGGTGTGCTGCTGGGCTATGAGATCGTGGATGTGTGCTACATCTCCAACAATGTCCAGCCGGTGCTCTACTTCCTGGCACACGAGGACAACCTCCTTCCCATCCAAGAGGACTACAGTAACTACATTTCCCGTGTGGTGGCTGTCATTGGCCCTGACAACTCCGAGTCTGTCATGACTGTGGCCAACTTCCTCTCCCTATTTCTCCTTCCACAG --referenceAA SSLLPGVLLGYEIVDVCYISNNVQPVLYFLAHEDNLLPIQEDYSNYISRVVAVIGPDNSESVMTVANFLSLFLLPQ --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: ECD1 Fragment B read 2: python2.7 Fused_read_aligner.py --path express1_fragB_R2/ --infile T1R2_ECD1_express1_R2.fast_R2_qc1 --referenceDNA GACAATGGCCAGCTGCTTGGCGAGCGCGTGGCCCGGCGCGACATCTGCATCGCCTTCCAGGAGACGCTGCCCACACTGCAGCCCAACCAGAACATGACGTCAGAGGAGCGCCAGCGCCTGGTGACCATTGTGGACAAGCTtCAGCAGAGCACAGCGCGCGTCGTGGTCGTGTTCTCGCCCGACCTGACCCTGTACCACTTCTTC --referenceAA DNGQLLGERVARRDICIAFQETLPTLQPNQNMTSEERQRLVTIVDKLQQSTARVVVVFSPDLTLYHFF --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: ECD2 Fragment A read 1: python2.7 Fused_read_aligner.py --path express1_fragA_R1/ --infile T1R2_ECD2_express1_R1.fast_R1_qc1 --referenceDNA AATGAGGTGCTGCGCCAGAACTTCACTGGCGCCGTGTGGATCGCCTCCGAGTCCTGGGCCATCGACCCGGTCCTGCACAACCTCACGGAGCTGCGCCACTTGGGCACCTTCCTGGGCATCACCATCCAGAGCGTGCCCATCCCGGGCTTCAGTGAGTTCCGCGAGTGGGGCCCACAGGCTGGGCCGCCACCCCTCAGCAGGACCAGCCAGAGCTATACCTGCAACCAGGAG --referenceAA NEVLRQNFTGAVWIASESWAIDPVLHNLTELRHLGTFLGITIQSVPIPGFSEFREWGPQAGPPPLSRTSQSYTCNQE --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: ECD2 Fragment A read 2: python2.7 Fused_read_aligner.py --path express1_fragA_R2/ --infile T1R2_ECD2_express1_R2.fast_R2_qc1 --referenceDNA TACCCCTGGCAGCTGCTcGAGGAGATCTGGAAGGTCAACTTCACTCTCCTGGACCACCAAATCTTCTTCGACCCGCAAGGGGACGTGGCTCTGCACTTGGAGATTGTCCAGTGGCAATGGGACCGGAGCCAGAATCCCTTCCAGAGCGTCGCCTCCTACTACCCCCTGCAGCGACAGCTGAAGAACATCCAAGACATCTCC --referenceAA YPWQLLEEIWKVNFTLLDHQIFFDPQGDVALHLEIVQWQWDRSQNPFQSVASYYPLQRQLKNIQDIS --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: ECD2 Fragment B read 1: python2.7 Fused_read_aligner.py --path express1_fragB_R1/ --infile T1R2_ECD2_express1_R1.fast_R1_qc1 --referenceDNA TGCAACCAGGAGTGCGACAACTGCCTGAACGCCACCTTGTCCTTCAACACCATTCTCAGGCTCTCTGGGGAGCGTGTCGTCTACAGCGTGTACTCTGCGGTCTATGCTGTGGCCCATGCCCTGCACAGCCTCCTCGGCTGTGACAAAAGCACCTGCACCAAGAGGGTGGTCTACCCCTGGCAGCTGCTcGAGGAGATCTGGAAGGTCAACTTCACTCTCCTGGACCAC --referenceAA CNQECDNCLNATLSFNTILRLSGERVVYSVYSAVYAVAHALHSLLGCDKSTCTKRVVYPWQLLEEIWKVNFTLLDH --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: ECD2 Fragment B read 2: python2.7 Fused_read_aligner.py --path express1_fragB_R2/ --infile T1R2_ECD2_express1_R2.fast_R2_qc1 --referenceDNA TGGCACACCATCAACAACACGATCCCTATGTCCATGTGTTCCAAGAGGTGCCAGTCAGGGCAAAAGAAGAAGCCTGTGGGCATCCACGTCTGCTGCTTCGAGTGCATCGACTGCCTTCCCGGCACCTTCCTCAACCACACTGAAGATGAATATGAATGCCAGGCCTGCCCGAATAACGAGTGGTCCTACCAGAGTGAGACC --referenceAA WHTINNTIPMSMCSKRCQSGQKKKPVGIHVCCFECIDCLPGTFLNHTEDEYECQACPNNEWSYQSET --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: TMD Fragment A read 1: python2.7 Fused_read_aligner.py --path express1_fragA_R1/ --infile T1R2_TMD_express1_R1.fast_R1_qc1 --referenceDNA TCCTGCTTCAAGCGGCAGCTGGTCTTCCTGGAATGGCATGAGGCACCCACCATCGCTGTGGCCCTGCTGGCCGCCCTGGGCTTCCTCAGCACCCTGGCCATCCTGGTGATATTCTGGAGGCACTTCCAGACACCCATcGTaCGCTCGGCTGGGGGCCCCATGTGCTTCCTGATGCTGACACTGCTGCTGGTGGCATACATGGTGGTC --referenceAA SCFKRQLVFLEWHEAPTIAVALLAALGFLSTLAILVIFWRHFQTPIVRSAGGPMCFLMLTLLLVAYMVV --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: TMD Fragment A read 2: python2.7 Fused_read_aligner.py --path express1_fragA_R2/ --infile T1R2_TMD_express1_R2.fast_R2_qc1 --referenceDNA TTCCAGATCGTCTGCGCCTTCAAGATGGCCAGCCGCTTCCCACGCGCCTACAGCTACTGGGTCCGCTACCAGGGGCCCTACGTCTCTATGGCATTTATCACGGTACTCAAAATGGTCATTGTGGTAATTGGCATGCTGGCCACGGGCCTCAGTCCCACCACCCGTACTGACCCCGATGACCCCAAGATCACAATTGTCTCCTGTAATCCCAACTACCGC --referenceAA FQIVCAFKMASRFPRAYSYWVRYQGPYVSMAFITVLKMVIVVIGMLATGLSPTTRTDPDDPKITIVSCNPNYR --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: TMD Fragment B read 1: python2.7 Fused_read_aligner.py --path express1_fragB_R1/ --infile T1R2_TMD_express1_R1.fast_R1_qc1 --referenceDNA CTGCTGCTGGTGGCATACATGGTGGTCCCGGTGTACGTGGGGCCGCCCAAGGTCTCCACCTGCCTCTGCCGCCAGGCCCTCTTTCCCCTCTGCTTCACAATCTGCATCTCCTGTATCGCCGTGCGTTCTTTCCAGATCGTCTGCGCCTTCAAGATGGCCAGCCGCTTCCCACGCGCCTACAGCTACTGGGTCCGCTACCAGGGGCCCTACGTCTCTATG --referenceAA LLLVAYMVVPVYVGPPKVSTCLCRQALFPLCFTICISCIAVRSFQIVCAFKMASRFPRAYSYWVRYQGPYVSM --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: TMD Fragment B read 2: python2.7 Fused_read_aligner.py --path express1_fragB_R2/ --infile T1R2_TMD_express1_R2.fast_R2_qc1 --referenceDNA TGTAATCCCAACTACCGCAACAGCCTGCTGTTCAACACCAGCCTGGACCTGCTGCTCTCAGTGGTGGGTTTCAGCTTCGCCTACATGGGCAAAGAGCTGCCCACCAACTACAACGAGGCCAAGTTCATCACCCTCAGCATGACCTTCTATTTCACCTCATCCGTCTCCCTCTGCACCTTCATGTCTGCCTACAGCGGGGTGCTGGTCACCATCGTGGAC --referenceAA CNPNYRNSLLFNTSLDLLLSVVGFSFAYMGKELPTNYNEAKFITLSMTFYFTSSVSLCTFMSAYSGVLVTIVD --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: TMD Fragment C read 1: python2.7 Fused_read_aligner.py --path express1_fragC_R1/ --infile T1R2_TMD_express1_R1.fast_R1_qc1 --referenceDNA GCCAGCCGCTTCCCACGCGCCTACAGCTACTGGGTCCGCTACCAGGGGCCCTACGTCTCTATGGCATTTATCACGGTACTCAAAATGGTCATTGTGGTAATTGGCATGCTGGCCACGGGCCTCAGTCCCACCACCCGTACTGACCCCGATGACCCCAAGATCACAATTGTCTCCTGTAATCCCAACTACCGCAACAGCCTGCTGTTCAACACCAGCCTG --referenceAA ASRFPRAYSYWVRYQGPYVSMAFITVLKMVIVVIGMLATGLSPTTRTDPDDPKITIVSCNPNYRNSLLFNTSL --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: TMD Fragment C read 2: python2.7 Fused_read_aligner.py --path express1_fragC_R2/ --infile T1R2_TMD_express1_R2.fast_R2_qc1 --referenceDNA GTCTCCCTCTGCACCTTCATGTCTGCCTACAGCGGGGTGCTGGTCACCATCGTGGACCTCTTGGTCACTGTGCTCAACCTCCTGGCCATCAGCCTGGGCTACTTCGGCCCCAAGTGCTACATGATCCTCTTCTACCCGGAGCGCAACACGCCCGCCTACTTCAACAGCATGATCCAGGGCTACACCATG --referenceAA VSLCTFMSAYSGVLVTIVDLLVTVLNLLAISLGYFGPKCYMILFYPERNTPAYFNSMIQGYTM --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
MapCounts script: Example: python mapCounts.py --path express1_fragA_R1/ --infile T1R2_TMD_express1_R1.fast_R1_qc1_PRO_qc2
MapRatios script: Example: python mapRatios.py --path ratios_directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: Example: python mapParts.py --path ratios_directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script: Example: python mapUnlink.py --path ratios/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size ##
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Data was then assembled from the different fragments/reads to span the full sequence in Excel.  Where there was overlap, real enrichment ratios were averaged and converted back to log(base2). Maximum depletion was set to log(base2) enrichment ratio = -4.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library.

source_name: Synthetic coding sequences

growth_protocol: Expi293F cells stably expressing myc-T1R3 cultured in Expi293 Expression Medium (Life Technologies)

extract_protocol:
Total RNA was harvested from sorted cells using GeneJet RNA Purification Kit (Thermo Scientific) and cDNA prepared using Accuscript Hi-Fi (Agilent Genomics) primed with a gene-specific primer: natT1R2_882_ECD1_R (AGTGAAGTTCTGGCGCAG, ECD1 library), natT1R2_1682_ECD2_R (CATTCCAGGAAGACCAGC, ECD2 library), and EBV_reverse (GTGGTTTGTCCAAACTCATC, TMD library).
In the first round of PCR (18 cycles), the T1R2 coding sequences were amplified as overlapping fragments of ~800 bp each.
Primer pair (ECD1 Library Fragment A): MiSeq_HA-SP_F (TCTTTCCCTACACGACGCTCTTCCGATCTACTACAAGGATGACGACGAC) and MiSeq_T1R2_670_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCAAGCAGCTGGCCATTGTC)
Primer pair (ECD1 Library Fragment B): MiSeq_T1R2_234_F (TCTTTCCCTACACGACGCTCTTCCGATCTGGTGGAGGAGATCAACAATG) and MiSeq_T1R2_882_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGTGAAGTTCTGGCGCAGCA)
Primer pair (ECD2 Library Fragment A): MiSeq_T1R2_835_F (TCTTTCCCTACACGACGCTCTTCCGATCTGACCCTGTACCACTTCTT) and MiSeq_T1R2_1466_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTGTTGTTGATGGTGTGCCA)
Primer pair (ECD2 Library Fragment B): MiSeq_T1R2_1054_F (TCTTTCCCTACACGACGCTCTTCCGATCTAGGACCAGCCAGAGCTATAC) and MiSeq_T1R2_1673_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGACCAGCTGCCGCTTGAA)
Primer pair (TMD Library Fragment A): MiSeq_T1R2_1617_F (TCTTTCCCTACACGACGCTCTTCCGATCTGAATAACGAGTGGTCCTACC) and MiSeq_T1R2_2195_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTGTTGAACAGCAGGCTGTT)
Primer pair (TMD Library Fragment B): MiSeq_T1R2_1807_F (TCTTTCCCTACACGACGCTCTTCCGATCTATGTGCTTCCTGATGCTGAC) and MiSeq_T1R2_2396_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGAGCACAGTGACCAAGAG)
Primer pair (TMD Library Fragment C): MiSeq_T1R2_1963_F (TCTTTCCCTACACGACGCTCTTCCGATCTATCGTCTGCGCCTTCAAGAT) and MiSeq_pCEP4_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTATCATGTCTGGATCCGG)
In a second round of PCR (15 cycles), Illumina adaptors and experiment-specific barcodes were added.
Primer pair for adding I5 and I7 Illumina adaptors: MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced with HiSeq 2500 instruments using a 2x250 nt paired end protocol, though data is analyzed as single reads.

treatment_protocol: Cells expressing DNA libraries of T1R2 and stably expressing T1R3 were FACS sorted for surface expression of T1R2 or T1R3.  Three single site-saturation mutagenesis libraries were created, spanning residues 22-285 (ECD1 library), 286-549 (ECD2 library), and 550-836 (TMD library).

tag: protein

tag: sort gate 1

value: Top 100% for T1R2 surface expression (anti-FLAG-Cy3 staining); square gate in Cy3-vs-Alexa 647 plot

tag: sort gate 2

value: Top 20% for T1R3 surface expression (anti-myc-Alexa 647 staining); sloped gate in Cy3-vs-Alexa 647 plot

tag: # collected cells


title: control, no neuronal degeneration post mortem, B64

status: Public on Dec 01 2018

type: genomic

city: Evry

first: Jorg

last: Tost

address: 2 rue Gaston Cremieux

country: France

institute: CEA-Institut de Genomique, Centre National de Genotypage

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human Methylation 450 K bead arrays (Illumina Inc., San Diego, CA). Processing was done according to the manufacturer’s protocol using an automated pipeline.  of bisulfite-treated DNA was analyzed using the Infinium  Human Methylation 450 K bead arrays spanning approximately  over 480,000 CpG sites/sample (Illumina Inc., San  Diego, CA). Processing was done according to the manufacturer’s  protocol using an automated pipeline, and the  arrays were scanned on an Illumina iScan platform (Illumina  Inc., San Diego, CA) established at the Life & Brain  Center (Bonn, Germany)

data_processing:
Subset quantile normalization, revised version of Touleimat & tost, Epigenomics 2012
The normalized.txt contains normalized Beta values.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: control_frontal cortex, post mortem tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from post-mortem brain samples using Qiagen DNeasy Kit according to standard instructions

tag: subject group

value: control

tag: subject status

value: no neuronal degeneration post mortem

tag: subject id

tag: gender

value: male

tag: age at death

tag: tssue

value: frontal cortex, post mortem tissue

tag: molecule subtype

value: bisulfite converted DNA from brain tissue


title: T1R2_TMD Expression Sorted Library; replicate 2

type: SRA

country: USA

description: Deep mutational scan for surface expression of T1R2

library_source: transcriptomic

molecule: total RNA


title: T1R2_TMD Dimer_Sorted Library; replicate 2


title: 43706: tubulovillous adenoma of Patient 41665

type: RNA

city: Beerse

first: Joke

last: Reumers

address: Turnhoutseweg 32

department: DPDS

country: Belgium

institute: Janssen R&D

hyb_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

data_processing: Data were analyzed using Bioconductor 3.2 running on R 3.2.2. Probeset expression measures were calculated using the Affymetrix package’s Robust Multichip Average (RMA) default method.

label: biotin

source_name: Patient 41665

extract_protocol: Qiagen RNAeasy FFPE

tag: patient id

tag: age

tag: tissue

value: colorectal adenoma

tag: adenomadiagnosis

value: tubulovillous adenoma


title: 43659: tubulovillous adenoma of Patient 41668

scan_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

source_name: Patient 41668

value: female


title: Null-1-Control_1

city: Concepción

first: Carlos

last: Farkas

state: Biobío

address: Chacabuco 1140, 1808

department: Bioquímica y Biología Molecular

country: Chile

institute: Universidad de Concepción (UDEC)

description: mRNA depleted of rRNA

data_processing:
Base calling and quality scoring were performed with the Real-Time Analysis system (RTA v2)
Sequenced reads were trimmed for adaptor sequence and then mapped to mm10 whole genome using HISAT2 v2.1.0 (default settings) in the Main Galaxy Platform (https://usegalaxy.org/).
Variant calling was perfomed in every sample using the freebayes parallel script : freebayes-parallel <(fasta_generate_regions.py mm10.fai 100000) 40 -f mm10 -b *.sorted.bam > *.sorted.bam.vcf, where * correspond to WT or KO samples (see https://github.com/ekg/freebayes/blob/master/scripts/freebayes-parallel).
Gene counts per sample were obtained with the HTSeq count script (v0.9.1) implemented in the Galaxy platform against mm10 build. Count Table was constructed in R and normalized with the RUVSeq code (see https://bioconductor.org/packages/release/bioc/html/RUVSeq.html). Differential expression was tested with the edgeRun code in R (see https://cran.r-project.org/web/packages/edgeRun/index.html) between WT and KO samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with gene counts per sample.

organism: Mus musculus

source_name: Mouse Embryonic Fibroblasts

growth_protocol: DMEM supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, GE Healthcare HyClone), 1% glutamine (Invitrogen), and 0.5% penicillin/streptomycin (Invitrogen)

extract_protocol:
Total RNA was extracted from each sample with the RNeasy Plus Mini Kit (Qiagen) according to manufacturer's instructions
RNA-Seq libraries were prepared at University of Cambridge sequencing facility (UK) using the TruSeq Stranded mRNA LT Sample Prep Kit (Catalog IDs: RS-122-2101, RS-122-2102). 4 µg of total RNA per sample was depleted of rRNA with the Ribo-Zero Gold rRNA Removal Kit (Illumina) and messenger RNA was further enriched with the Truseq Stranded mRNA Sample Preparation Kit (Illumina). All samples (10) were sequenced using the NextSeq 500 machine with high output configuration (400 million reads, 1x150 bp)

treatment_protocol: Doxorubicin 1 µM (Sigma Aldrich) for sixteen hours

tag: cell type

value: Primary MEFs 13.5 days post coitum

tag: passages

value: three

tag: strain

value: Mixed C57BL/6J-129P2OlaHsd


title: Null-1-16h-Doxo_2

description: mRNA depleted of rRNA


title: control, no neuronal degeneration post mortem, B63

scan_protocol: the arrays were scanned on an Illumina iScan platform


title: 43413: tubulovillous adenoma of Patient 41670

source_name: Patient 41670

label_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)


title: control, no neuronal degeneration post mortem, B62


title: 43436: tubulovillous adenoma of Patient 41669

source_name: Patient 41669


title: T1R2_TMD Expression Sorted Library; replicate 1

tag: protein

tag: sort gate 1


title: mNSCLC-H2AK5ac_4

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

country: Germany

institute: Max Delbrüch Center

description:
KP primary tumors
k5_61

library_source: genomic

data_processing:
bcl2fastq converter (version v2.17.1.14)
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 version 2.3.4.3
Genome_build: mm10
Supplementary_files_format_and_content: BigWig were generated using bedtools genomecov (v2.26) and wigToBigWig (v.4)

source_name: in vivo

growth_protocol: NSCLC cells were tail vein inected in Nude mice

extract_protocol:
Trypsin/Collegenase/Hyarulonydase/DNaseI digestion followed by SDS buffer lysis. ChIP-seq was performed as previously described (Serresi et al., 2016).
Libraries were prepared according to Illumina's instructions.

tag: disease state

value: NSCLC

value: lung tumor

tag: genotype

tag: chip antibody

value: anti-h2ak5ac  c15410215 Diagenode


title: 43350: tubulovillous adenoma of Patient 41671

source_name: Patient 41671


title: mNSCLC-H2AK5ac_3

description:
KP primary tumors
k5_60


title: control, no neuronal degeneration post mortem, B61

tag: subject group

tag: subject status

tag: subject id


title: 43357: tubular adenoma of Patient 41673

source_name: Patient 41673

tag: gender

value: tubular adenoma


title: 43359: tubulovillous adenoma of Patient 41674

source_name: Patient 41674


title: mNSCLC-H2AK5ac_2

description:
KP primary tumors
k5_59


title: control, no neuronal degeneration post mortem, B60

tag: age at death

tag: tssue

tag: molecule subtype


title: mNSCLC-H2AK5ac_1

description:
KP primary tumors
k5_58


title: control, no neuronal degeneration post mortem, B59


title: T1R2_ECD2 Expression Sorted Library; replicate 2

value: Top 55% for T1R2 surface expression (anti-FLAG-Cy3 staining); square gate in Cy3-vs-Alexa 647 plot

tag: sort gate 2

tag: # collected cells


title: T1R2_ECD2 Dimer_Sorted Library; replicate 1

value: Top 20% for T1R3 surface expression (anti-myc-Alexa 647 staining); sloped gate in Cy3-vs-Alexa 647 plot


title: mNSCLC-H3K27ac_3

description:
KP primary tumors
k27_60

tag: cell type

value: anti-H3K27ac ab4729 Abcam


title: T1R2_ECD2 Expression Sorted Library; replicate 1


title: control, no neuronal degeneration post mortem, B57

value: control

value: no neuronal degeneration post mortem


title: T1R2_ECD1 Dimer_Sorted Library; replicate 2


title: 43367: tubulovillous adenoma of Patient 41676

source_name: Patient 41676

tag: patient id

tag: age

tag: tissue

tag: adenomadiagnosis


title: T1R2_ECD2 Dimer_Sorted Library; replicate 2

tag: protein

tag: sort gate 1


title: 43437: tubulovillous adenoma of Patient 41675

source_name: Patient 41675

value: male


title: control, no neuronal degeneration post mortem, B56

value: frontal cortex, post mortem tissue

value: bisulfite converted DNA from brain tissue


title: 43431: serrated adenoma of Patient 41672

source_name: Patient 41672

value: colorectal adenoma

value: serrated adenoma


title: T1R2_ECD1 Expression Sorted Library; replicate 2


title: T1R2_ECD1 Dimer_Sorted Library; replicate 1


title: mNSCLC-H3K27ac_2

description:
KP primary tumors
k27_59

tag: disease state

tag: genotype

tag: chip antibody


title: mNSCLC-H3K27ac_1

description:
KP primary tumors
k27_58


title: T1R2_ECD1 Expression Sorted Library; replicate 1


title: control, no neuronal degeneration post mortem, B55

tag: subject group

tag: subject status

tag: subject id


title: 43439: tubulovillous adenoma of Patient 41677

source_name: Patient 41677

tag: gender

value: female

value: tubulovillous adenoma


title: P4 untreated 3 (P4_U_3)

city: Boston

first: Rory

last: Kirchner

state: MA

address: 677 Huntington Ave

department: Department of Biostatistics

institute: Harvard T.H. Chan School of Public Health

description: Cochlear sensory epithelia were dissected out and incubated with Cell Recovery Solution (Corning) to separate hair cells and supporting cells from mesenchyme and neurons. RNA was extracted from hair cells and supporting cells alone. Every sample is from 2 ears of 1 pup.

data_processing:
Reads were aligned to mm10 augmented with Ensembl gene build 75 with STAR v2.5.2b
Reads and alignments were assessed for quality using a combination of FastQC, Qualimap and custom scripts
Counts of reads per gene were generated using FeatureCounts
Transcripts Per Million (TPM) measurements were generated using Sailfish v0.10.1
Transcript counts were collapsed to gene level counts using Tximport
Differential expression was evaluated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: CSV (DESeq2 normalized counts)

source_name: β-catenin-flox(Exon3)/+ (no Cre)

growth_protocol: Mice were maintained at MEEI ACF accodring to IACUC regulations

extract_protocol:
Cochlear sensory epithelia were dissected out and incubated with Cell Recovery Solution (Corning) to separate hair cells and supporting cells from mesenchyme and neurons. RNA was extracted using RNeasy Micro Kit (Qiagen) from hair cells and supporting cells alone. Every sample is from 2 ears of 1 pup.
cDNA was synthesized from 2.5 ng of RNA using SMARTer V4 Kit (Clontech). Fragmentation was done using M220 Focused-Ultrasonicator (Covaris) and 2 ng of sheared cDNA were taken for library preparation using ThruPLEX DNA-seq kit (Rubicon Genomics)

treatment_protocol: For Cre activation in neonatal mice, mothers were given 100 μl tamoxifen (50 μg/μl, Sigma-Aldrich) via intraperitoneal injection 1 or 4 days after delivery. Sox2-CreER; β-cateninflox(Exon3)/+ pups and β-cateninflox(Exon3)/+ littermate controls were exposed to tamoxifen at P1 or P4 through the mother’s milk and sacrificed 72 hours later at P4 or P7, respectively.

tag: strain

value: Mixed C57BL/6 and CD1

value: Cochlear sensory epithelium

value: Tamoxifen at P4, harvested at P7


title: control, no neuronal degeneration post mortem, B58

tag: age at death

tag: tssue

tag: molecule subtype


title: 43406: tubulovillous adenoma of Patient 41679

source_name: Patient 41679

tag: patient id


title: mNSCLC-H3K27ac_4

description:
KP primary tumors
k27_61

value: NSCLC

tag: cell type

value: lung tumor


title: control, no neuronal degeneration post mortem, B24


title: T1R2 TMD Naive Library

description:
plasmid DNA
Naïve T1R2 SSM library TMD (a.a. 550-836)

source_name: Synthetic coding sequences

tag: sort gate 2

tag: # collected cells


title: T1R2 ECD2 Naive Library

description:
plasmid DNA
Naïve T1R2 SSM library ECD2 (a.a. 286-549)

tag: protein


title: P4 untreated 2 (P4_U_2)

tag: tissue

tag: age


title: 43713: villous adenoma of Patient 41680

source_name: Patient 41680

tag: adenomadiagnosis

value: villous adenoma


title: 43703: tubulovillous adenoma of Patient 41682

source_name: Patient 41682


title: control, no neuronal degeneration post mortem, B23

source_name: control_frontal cortex, post mortem tissue


title: 43392: tubulovillous adenoma of Patient 41678

source_name: Patient 41678


title: P4 untreated 1 (P4_U_1)


title: P4 treated 2 (P4_T_2)

data_processing:
Reads were aligned to mm10 augmented with Ensembl gene build 75 with STAR v2.5.2b
Reads and alignments were assessed for quality using a combination of FastQC, Qualimap and custom scripts
Counts of reads per gene were generated using FeatureCounts
Transcripts Per Million (TPM) measurements were generated using Sailfish v0.10.1
Transcript counts were collapsed to gene level counts using Tximport
Differential expression was evaluated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: No DESeq2 normalized counts are provided for this sample because the experiment was supposed to knock out exon 3 of Cttnb1, but the knockdown had varying efficacy and this sample showed no evidence of knockdown when we looked at the RNA-seq data.

source_name: Sox2-CreER/+; β-catenin-flox(Exon3)/+


title: P4 treated 3 (P4_T_3)


title: control, no neuronal degeneration post mortem, B22


title: Mia Palbo 2

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description:
PDAC_FPKM.txt
S72_S72_L001_R1_001

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (29), aligned to the human genome using STAR (30), and quantified transcript counts using HTSeq (31). Raw read counts were normalized to FPKM value for analysis.
Genome_build: Reads were aligned to the transcriptome (hg19, GRCh37.75)
Supplementary_files_format_and_content: Tab-delimited text file includes normalized FPKM value for each sample

source_name: Pancreatic cancer cell line

growth_protocol: Cells were maintained in DMEM or RPMI supplemented with 10%  FBS and 100 IU/ml penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a fpkm matrix of transcript counts.

treatment_protocol: Cells were treated for 8 days with vehicle (DMSO), trametinib (25 nM), palbociclib (500nM), or both in combination. Drug media was changed every 3 days.

tag: cell line

tag: treatment

value: Palbociclib


title: control, no neuronal degeneration post mortem, B21

tag: subject group

tag: subject status


title: T1R2 ECD1 Naive Library

description:
plasmid DNA
Naïve T1R2 SSM library ECD1 (a.a. 22-285)

tag: sort gate 1


title: control, no neuronal degeneration post mortem, B54

tag: subject id

tag: gender


title: control, no neuronal degeneration post mortem, B20

tag: age at death

tag: tssue


title: Mia Palbo 1

description:
PDAC_FPKM.txt
S71_S71_L001_R1_001


title: P4 treated 1 (P4_T_1)

tag: strain


title: 43384: tubulovillous adenoma of Patient 41684

source_name: Patient 41684

tag: patient id


title: 43432: tubulovillous adenoma of Patient 41685

source_name: Patient 41685


title: 43388: tubulovillous adenoma of Patient 41683

source_name: Patient 41683


title: P1 untreated 3 (P1_U_3)

value: Tamoxifen at P1, harvested at P4


title: 43426: tubulovillous adenoma of Patient 41686

source_name: Patient 41686


title: P1 untreated 2 (P1_U_2)


title: control, no neuronal degeneration post mortem, B18

value: control

tag: molecule subtype


title: Mia Combo 1

description:
PDAC_FPKM.txt
S69_S69_L001_R1_001

value: Combination


title: Mia Tramet 2

description:
PDAC_FPKM.txt
S68_S68_L001_R1_001

value: Trametinib


title: P1 untreated 1 (P1_U_1)


title: 43404: tubulovillous adenoma of Patient 41687

source_name: Patient 41687

value: male


title: control, no neuronal degeneration post mortem, B17

value: no neuronal degeneration post mortem

value: frontal cortex, post mortem tissue

value: bisulfite converted DNA from brain tissue


title: 43651: tubulovillous adenoma of Patient 41688

source_name: Patient 41688

value: female

value: colorectal adenoma


title: P1 treated 3 (P1_T_3)

value: Mixed C57BL/6 and CD1


title: control, no neuronal degeneration post mortem, B16


title: 43640: tubulovillous adenoma of Patient 41690

source_name: Patient 41690

value: tubulovillous adenoma


title: 43425: tubulovillous adenoma of Patient 41689

source_name: Patient 41689


title: Mia Vehicle 2

description:
PDAC_FPKM.txt
S66_S66_L001_R1_001

value: Vehicle


title: P1 treated 2 (P1_T_2)

value: Cochlear sensory epithelium


title: Mia Combo 2

description:
PDAC_FPKM.txt
S70_S70_L001_R1_001


title: P1 treated 1 (P1_T_1)


title: PANC-1 Combo 2

description:
PDAC_FPKM.txt
S64_S64_L001_R1_001


title: Mia Vehicle 1

description:
PDAC_FPKM.txt
S65_S65_L001_R1_001


title: control, no neuronal degeneration post mortem, B19


title: control, no neuronal degeneration post mortem, B15


title: 43641: tubulovillous adenoma of Patient 41691

source_name: Patient 41691


title: control, no neuronal degeneration post mortem, B13


title: PANC-1 Combo 1

description:
PDAC_FPKM.txt
S63_S63_L001_R1_001


title: 43438: tubulovillous adenoma of Patient 41694

source_name: Patient 41694


title: control, no neuronal degeneration post mortem, B12


title: Mia Tramet 1

description:
PDAC_FPKM.txt
S67_S67_L001_R1_001


title: control, no neuronal degeneration post mortem, B11


title: 43398: tubulovillous adenoma of Patient 41695

source_name: Patient 41695


title: PANC-1 Palbo 1

description:
PDAC_FPKM.txt
S61_S61_L001_R1_001


title: control, no neuronal degeneration post mortem, B14


title: control, no neuronal degeneration post mortem, B101


title: PANC-1 Tramet 2

description:
PDAC_FPKM.txt
S60_S60_L001_R1_001


title: control, no neuronal degeneration post mortem, B100


title: 43348: tubulovillous adenoma of Patient 41697

source_name: Patient 41697


title: PANC-1 Tramet 1

description:
PDAC_FPKM.txt
S59_S59_L001_R1_001


title: control, no neuronal degeneration post mortem, B10


title: 43381: tubulovillous adenoma of Patient 41693

source_name: Patient 41693


title: PANC-1 Vehicle 2

description:
PDAC_FPKM.txt
S58_S58_L001_R1_001


title: PANC-1 Palbo 2

description:
PDAC_FPKM.txt
S62_S62_L001_R1_001


title: control, no neuronal degeneration post mortem, B09

source_name: control_frontal cortex, post mortem tissue


title: 43399: tubulovillous adenoma of Patient 41698

source_name: Patient 41698


title: PANC-1 Vehicle 1

description:
PDAC_FPKM.txt
S57_S57_L001_R1_001


title: 8988T Combo 2

description:
PDAC_FPKM.txt
S56_S56_L001_R1_001


title: control, no neuronal degeneration post mortem, B08


title: 43631: tubulovillous adenoma of Patient 41699

source_name: Patient 41699


title: control, no neuronal degeneration post mortem, B07


title: control, no neuronal degeneration post mortem, B06


title: Muscle stem cells cultured in 10% FBS for 3 days

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: Fifteen micrograms of cRNA was hybridized to Affymetrix MOE_430_2 arrays, and arrays were washed and stained using an Affymetrix FS4500 fluidics station

scan_protocol: GeneChips were scanned using The Affymetrix GC3000 scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

source_name: MuSCs_10% FBS for 3 days

label_protocol: Twenty nanograms of total RNA was prepared for array analysis using Affymetrix 3’ IVT Express amplification reagents

growth_protocol: Mouse muscle stem cells were purified essentially as previously described (Cosgrove et al., 2014) using a FACS Aria 2, routinely yielding >95% CD34+α7 integrin+ cells from a single round of sorting.

extract_protocol: Total RNA was prepared with Qiagen RNeasy kits according to Qiagen's instructions

treatment_protocol: Muscle stem cells were cultured in 10% FBS plus or minus 100 ng/mL oncostatin M for 3 days

tag: strain background

tag: genotype/variation

value: wildtype

value: 8 weeks

value: muscle

tag: cell type

value: cultured muscle stem cells (MuSC)

tag: culture condition

value: 10% FBS for 3 days


title: Freshly isolated muscle stem cells

source_name: Freshly isolated_MuSCs

tag: age

tag: tissue

value: Freshly isolated muscle stem cells (MuSC)

value: none (freshly isolated)


title: 8988T Combo 1

description:
PDAC_FPKM.txt
S55_S55_L001_R1_001

source_name: Pancreatic cancer cell line

tag: cell line

tag: treatment

value: Combination


title: Muscle stem cells cultured in 10% FBS and 100 ng/mL oncostatin M for 3 days

source_name: MuSCs_10% FBS and 100 ng/mL oncostatin M for 3 days


title: 43365: tubular adenoma of Patient 41701

source_name: Patient 41701

tag: adenomadiagnosis

value: tubular adenoma


title: 8988T Palbo 2

description:
PDAC_FPKM.txt
S54_S54_L001_R1_001

value: Palbociclib


title: control, no neuronal degeneration post mortem, B05

tag: subject group

value: control

tag: subject status

value: no neuronal degeneration post mortem

value: frontal cortex, post mortem tissue

value: bisulfite converted DNA from brain tissue


title: 8988T Palbo 1

description:
PDAC_FPKM.txt
S53_S53_L001_R1_001


title: 8998T Tramet 2

description:
PDAC_FPKM.txt
S52_S52_L001_R1_001

value: Trametinib


title: control, no neuronal degeneration post mortem, B04

tag: subject id

tag: gender

value: male


city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

description: BMDC with CLIK148 pre-treatment, CpG stimulation, biological replicate 1

hyb_protocol: 200µl hybridization mix prepared from labeled cRNA fragments was hybridized to oligonucleotide arrays for 16h at 45°C. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0001.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

source_name: bone marrow-derived dendritic cells

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturer's protocol.

growth_protocol: Murine BMDC were generated from stem cell progenitors of BALB/c mice by culture with rGM-CSF in complete RMPI medium over 8 days, with feedings on days 3 and 6.

extract_protocol: Total RNA was isolated using Qiagen's RNeasy column system, following the manufacturer's instructions. RNA was eluted from the columns using 30µL of RNAse-free water

treatment_protocol: BMDC were pre-treated with 5 µM of CA074Me, CLIK148 or an equivalent volume of DMSO (0.01%) for 1h, then stimulated with CpG (25µg/mL) or TNF-alpha (500 U/mL)

value: anti TH1

value: BALB/c

value: bone marrow-derived dendritic cells


description: BMDC with CA074Me pre-treatment, TNF-alpha stimulation, biological replicate 2

value: anti TH2


title: 43722: tubular adenoma of Patient 41706

source_name: Patient 41706

value: colorectal adenoma


title: 43656: tubulovillous adenoma of Patient 41705

source_name: Patient 41705

value: female

value: tubulovillous adenoma


title: 43397: tubulovillous adenoma of Patient 41704

source_name: Patient 41704


title: 43708: tubulovillous adenoma of Patient 41703

source_name: Patient 41703


title: 43346: tubulovillous adenoma of Patient 41700

source_name: Patient 41700


description: BMDC with CLIK148 pre-treatment, CpG stimulation, biological replicate 2


title: control, no neuronal degeneration post mortem, B03

tag: age at death

tag: tssue


title: 8998T Tramet 1

description:
PDAC_FPKM.txt
S51_S51_L001_R1_001


title: 8988T Vehicle 2

description:
PDAC_FPKM.txt
S50_S50_L001_R1_001

value: Vehicle


title: control, no neuronal degeneration post mortem, B02


description: BMDC with CA074Me pre-treatment, TNF-alpha stimulation, biological replicate 1

tag: strain


title: 43422: tubulovillous adenoma of Patient 41708

source_name: Patient 41708

tag: patient id


title: control, no neuronal degeneration post mortem, B01

tag: molecule subtype


title: 43711: tubular adenoma of Patient 41707

source_name: Patient 41707


description: BMDC with DMSO pre-treatment, CpG (pro-Th1) stimulation, biological replicate 2

value: pro TH1


description: BMDC with DMSO pre-treatment, TNF-alpha (pro-Th2) stimulation, biological replicate 2

value: pro TH2


title: 8988T Vehicle 1

description:
PDAC_FPKM.txt
S49_S49_L001_R1_001


description: BMDC with DMSO pre-treatment, TNF-alpha (pro-Th2) stimulation, biological replicate 1


title: H460 Combo 2

description:
NSCLC_FPKM.txt
A24_S120_L002_R1_001

source_name: Lung cell line

value: Combination


description: BMDC with DMSO pre-treatment, CpG (pro-Th1) stimulation, biological replicate 1


title: 43395: tubulovillous adenoma of Patient 41709

source_name: Patient 41709


title: H460 Trametb 2

description:
NSCLC_FPKM.txt
A22_S118_L002_R1_001


description: BMDC with CA074Me pre-treatment, no further stimulation, biological replicate 2

value: CA074 control


title: 43373: tubulovillous adenoma of Patient 41711

source_name: Patient 41711


title: H460 Palbo 2

description:
NSCLC_FPKM.txt
A23_S119_L002_R1_001

value: Palbociclib


title: 43412: tubulovillous adenoma of Patient 41710

source_name: Patient 41710


title: H460 Vehicle 2

description:
NSCLC_FPKM.txt
A21_S117_L002_R1_001


title: 43368: tubulovillous adenoma of Patient 41713

source_name: Patient 41713


description: BMDC with CLIK148 pre-treatment, no further stimulation, biological replicate 2

value: CLIK control


title: H460 Combo 1

description:
NSCLC_FPKM.txt
A20_S116_L002_R1_001


title: 43407: tubulovillous adenoma of Patient 41712

source_name: Patient 41712


description: BMDC with CLIK148 pre-treatment, no further stimulation, biological replicate 1


title: 43702: tubulovillous adenoma of Patient 41714

source_name: Patient 41714


title: 43369: adenomatous polyp of Patient 41715

source_name: Patient 41715

value: adenomatous polyp


description: BMDC with DMSO pre-treatment (control), no further stimulation, biological replicate 2

value: DMSO control


description: BMDC with CA074Me pre-treatment, no further stimulation, biological replicate 1


title: H460 Tramet 1

description:
NSCLC_FPKM.txt
A18_S114_L002_R1_001

value: Trametinib


title: H460 Vehicle 1

description:
NSCLC_FPKM.txt
A17_S113_L002_R1_001


description: BMDC with DMSO pre-treatment (control), no further stimulation, biological replicate 1


title: H2030 Combo 2

description:
NSCLC_FPKM.txt
A16_S112_L002_R1_001


title: H2030 Palbo 2

description:
NSCLC_FPKM.txt
A15_S111_L002_R1_001


title: 43372: tubulovillous adenoma of Patient 41716

source_name: Patient 41716

value: male


title: H2030 Tramet 2

description:
NSCLC_FPKM.txt
A14_S110_L002_R1_001


title: 43405: tubular adenoma of Patient 41719

source_name: Patient 41719

value: tubular adenoma


title: 43428: adenomatous polyp of Patient 41721

source_name: Patient 41721


title: ASO_v25_GAPDH_ORF rep2

city: STANFORD

first: Jin

middle: Billy

last: Li

address: 300 Pasteur Dr.

department: Genetics

institute: Stanford University

data_processing:
Raw reads were filtered using Trim Galore! to remove low quality and adaptor bases. Reads shorter than 16nt were discarded.
Filtered reads were mapped to hg19 reference genome sequences using STAR v2.4.2a with parameters: --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
RNA editing level was quantified by counting the ratio of the number of G-containing reads over the number of all reads mapped to each loci (as described in PMID: 29022589)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited plain txt with header information. Editing level of each site is in the last column

molecule: polyA RNA

source_name: HeLa

extract_protocol:
RNA was isolated with the RNeasy MinElute Kit (Qiagen, Germany), treated with DNaseI, incubated with an RNA strand reverse complementary to the respective ASO and heated to 95°C for 3 min and purified again with the RNeasy MinElute Kit. Purified RNA was delivered to CeGaT (Germany) for Poly(A)+ mRNA sequencing
The library was prepared from 200 ng RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA)

value: HeLa

tag: genotype

value: wild type

value: ASO for RNA editing


title: ASO_v25_GAPDH_ORF_+IFN rep1

value: ASO for RNA editing + IFN


title: ASO_v25_GAPDH_ORF_+IFN rep2


title: 43718: tubular adenoma of Patient 41717

source_name: Patient 41717

value: female

value: colorectal adenoma


title: ASO_v25_GAPDH_ORF rep1


title: H460 Palbo 1

description:
NSCLC_FPKM.txt
A19_S115_L002_R1_001


title: 43652: villous adenoma of Patient 41722

source_name: Patient 41722

value: villous adenoma


title: 43638: tubulovillous adenoma of Patient 41718

source_name: Patient 41718

value: tubulovillous adenoma


title: 43636: tubulovillous adenoma of Patient 41720

source_name: Patient 41720


title: high dose 1

description:
Sample name: Pool 6
male hippocampus from mice treated with 100 mg/d/kg Venlafaxine

hyb_protocol: 200µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C to GeneChip Mouse Genome 430 2.0 arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0001.

source_name: RNA pool from high dose treated animal hippocampi

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: male DBA/2 mice were single housed under standard conditions (21 °C ± 1°C, humidity 50 - 55 %, 12 h light-dark cycle, standard chow ad libitum) and via their drinking water ingested Venlafaxine (0 / 30 / 100 mg/kg/d) over the time period of one month. In the end of the experiment mice were narcotized with isofluran, killed by head removal and brains taken out of the skull.

extract_protocol: Total RNA was isolated with the RNeasy Mini kit (Qiagen) according to the  manufacturer's protocol.

treatment_protocol: Mice in the verum groups received Venlafaxine via their drinking water. Drinking water was spiked with Venlafaxine depending on daily consumption and concentration in case was adapted on a weekly basis to ensure ingestion of the desired quantity.

tag: brain region

value: hippocampus

tag: hemisphere

value: left

tag: venlafaxine dose [kg/d/kg]

tag: rin

tag: hybridization date


title: H2030 Vehicle 2

description:
NSCLC_FPKM.txt
A13_S109_L002_R1_001

source_name: Lung cell line

tag: cell line

tag: treatment

value: Vehicle


title: control 2

description:
Sample name: Pool 7
male hippocampus from mice treated with 0 mg/d/kg Venlafaxine

source_name: RNA pool from control animal hippocampi


title: 43360: tubular adenoma of Patient 41723

source_name: Patient 41723

tag: age

tag: tissue

tag: adenomadiagnosis


title: low dose 2

description:
Sample name: Pool 4
male hippocampus from mice treated with 30 mg/d/kg Venlafaxine

source_name: RNA pool from low dose treated animal hippocampi

tag: gender


title: high dose 2

description:
Sample name: Pool 8
male hippocampus from mice treated with 100 mg/d/kg Venlafaxine

value: right


title: HSC3_resistant

city: Chiba

first: Yuki

last: Sawai

address: 1-8-1 Inohana,  Chuo-ku

department: Department of Oral Science

country: Japan

institute: Graduate School of Medicine, Chiba University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: HSC3, resistant

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: All of the cells were grown and maintained in Dulbecco's modified Eagle medium/DMEM (Sigma) supplemented with 10% fetal bovine serum and 50 units/mL penicillin and streptomycin at 37 °C, 5% CO2 in humidified atmosphere.

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega).

tag: cell type

value: Oral squamous cell carcinoma (OSCC) cell line

tag: cetuximab resistance

value: Resistant


title: HSC3_control

source_name: HSC3, control

value: Sensitive


title: Sa3_resistant

source_name: Sa3, resistant


title: low dose 1

description:
Sample name: Pool 3
male hippocampus from mice treated with 30 mg/d/kg Venlafaxine

tag: strain

value: male


title: control 1

description:
Sample name: Pool 1
male hippocampus from mice treated with 0 mg/d/kg Venlafaxine


title: ctrl+IFN rep2

value: control + IFN


title: SAS_resistant

source_name: SAS, resistant

value: SAS


title: H2030 Combo 1

description:
NSCLC_FPKM.txt
A12_S108_L002_R1_001

value: Combination


title: 43421: tubulovillous adenoma of Patient 41726

source_name: Patient 41726

tag: patient id


title: 43699: tubulovillous adenoma of Patient 41724

source_name: Patient 41724


title: ctrl rep1

value: HeLa

value: wild type

value: control


title: H2030 Palbo 1

description:
NSCLC_FPKM.txt
A11_S107_L002_R1_001

value: Palbociclib


title: ctrl rep2


title: H2030 Tramet 1

description:
NSCLC_FPKM.txt
A10_S106_L002_R1_001

value: Trametinib


title: A549 Combo 2

description:
NSCLC_FPKM.txt
A08_S104_L002_R1_001


title: A549 Palbo 2

description:
NSCLC_FPKM.txt
A07_S103_L002_R1_001


title: H2030 Vehicle 1

description:
NSCLC_FPKM.txt
A09_S105_L002_R1_001


title: 43719: tubulovillous adenoma of Patient 41727

source_name: Patient 41727

value: female

value: colorectal adenoma

value: tubulovillous adenoma


title: A549 Tramet 2

description:
NSCLC_FPKM.txt
A06_S102_L002_R1_001


title: 43644: tubulovillous adenoma of Patient 41729

source_name: Patient 41729


title: A549 Vehicle 2

description:
NSCLC_FPKM.txt
A05_S101_L002_R1_001

value: Vehicle


title: 43701: villous adenoma of Patient 41728

source_name: Patient 41728

value: villous adenoma


title: 43415: tubulovillous adenoma of Patient 41732

source_name: Patient 41732


title: Sa3_control

source_name: Sa3, control

value: Oral squamous cell carcinoma (OSCC) cell line


title: 43408: tubulovillous adenoma of Patient 41730

source_name: Patient 41730


title: 43355: tubulovillous adenoma of Patient 41731

source_name: Patient 41731


title: TH17 CD161_pos 5017 medium

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

hyb_protocol: Hybridization was performed according to specifications in One-Color Microarray-Based Gene Expression Analysis Protocol

scan_protocol: The data was extracted using Agilent Feature Extraction Software version 10.7.3.1 with default parameters of protocol GE1_107_Sep09.

data_processing: Data preprocessing was performed using R/Bioconductor (version 3.6) Agi4x44PreProcess (version 1.22) package. Briefly, raw Feature Extractor data was loaded into R and further background corrected (method=”half”, offset=50), normalized (method=”quantile”) and filtered (wellaboveBG=60, isfound=60). Statistical analysis and DE extraction were peformed with limma package (version 3.34.6).

source_name: human blood

label_protocol: Labelling was performed with the one color (Cyanine 3-CTP) Low Input Quick Amp Labeling Kit (Agilent Technologies) accordinf to manufacturer protocol.

growth_protocol: Cells were kept in culture in RPMI 1640 medium supplemented with 10% FCS and 50 IU/ml recombinanat human IL-2.

extract_protocol: RNA was extracted using RNeasy Micro Kit - QIAGEN following manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer

treatment_protocol: Cells were analyzed either resting either after 6 hours stimulation with anti-CD2+anti-CD3+anti-CD28 coated beads.

value: T Helper Lymphocyte 17

tag: cd161 marker

value: positive

tag: clone


title: A549 Tramet 1

description:
NSCLC_FPKM.txt
A02_S98_L002_R1_001

source_name: Lung cell line


title: ctrl+IFN rep1

source_name: HeLa

tag: genotype


title: SAS_control

source_name: SAS, control

value: Sensitive


title: TH17 CD161_pos 4824 medium


title: TH17 CD161_pos 4859 medium


title: 43361: tubulovillous adenoma of Patient 41733

source_name: Patient 41733

value: male


title: 43354: villoglandular polyp of Patient 41734

source_name: Patient 41734

value: villoglandular polyp


title: TH17 CD161_pos 5017 aCD2/3/28 6h


title: A549 Combo 1

description:
NSCLC_FPKM.txt
A04_S100_L002_R1_001

value: Combination


title: A549 Vehicle 1

description:
NSCLC_FPKM.txt
A01_S97_L002_R1_001


title: TH17 CD161_pos 4824 aCD2/3/28 6h


title: A549 Palbo 1

description:
NSCLC_FPKM.txt
A03_S99_L002_R1_001


title: 43635: villous adenoma of Patient 41736

source_name: Patient 41736


title: 43424: sessile serrated adenoma of Patient 41735

source_name: Patient 41735

value: sessile serrated adenoma


title: TH17 CD161_pos 4805 medium


title: TH17 CD161_pos 4719 medium


title: TH1 CD161_pos 4853 aCD2/3/28 6h

value: T Helper Lymphocyte 1


title: 43374: adenovillous polyp of Patient 41740

source_name: Patient 41740

value: adenovillous polyp


title: 43393: tubulovillous adenoma of Patient 41737

source_name: Patient 41737


title: 43700: tubulovillous adenoma of Patient 41742

source_name: Patient 41742


title: TH1 CD161_pos 4853 medium


title: TH17 CD161_pos 4719 aCD2/3/28 6h


title: 43358: tubulovillous adenoma of Patient 41739

source_name: Patient 41739


title: TH17 CD161_pos 4805 aCD2/3/28 6h


title: TH1 CD161_pos 5055 aCD2/3/28 6h


title: TH1 CD161_pos 5055 medium


title: 43634: tubulovillous adenoma of Patient 41741

source_name: Patient 41741


title: 43403: adenovillous polyp of Patient 41738

source_name: Patient 41738


title: 43391: sessile serrated adenoma of Patient 41744

source_name: Patient 41744


title: 43379: tubulovillous adenoma of Patient 41747

source_name: Patient 41747


title: 43396: tubular adenoma of Patient 41749

source_name: Patient 41749

value: tubular adenoma


title: TH1 CD161_pos 4779 medium

source_name: human blood


title: TH17 CD161_pos 4859 aCD2/3/28 6h


title: 43378: tubulovillous adenoma of Patient 41746

source_name: Patient 41746


title: TH1 CD161_pos 4779 aCD2/3/28 6h


title: 43364: tubulovillous adenoma of Patient 41745

source_name: Patient 41745


title: TH1 CD161_pos 4701 aCD2/3/28 6h


title: TH1 CD161_pos 4844 aCD2/3/28 6h


title: TH1 CD161_pos 4844 medium


title: TH1 CD161_neg 4628 aCD2/3/28 6h

value: negative


title: 43705: tubular adenoma of Patient 41750

source_name: Patient 41750

value: female


title: 43362: tubulovillous adenoma of Patient 41748

source_name: Patient 41748

value: colorectal adenoma


title: 43347: serrated adenoma of Patient 41743

source_name: Patient 41743

value: serrated adenoma


title: TH1 CD161_neg 4628 medium


title: TH1 CD161_pos 4701 medium


title: TH1 CD161_neg 4613 aCD2/3/28 6h


title: 43710: tubulovillous adenoma of Patient 41754

source_name: Patient 41754

value: tubulovillous adenoma


title: 43401: tubular adenoma of Patient 41752

source_name: Patient 41752


title: 43414: tubulovillous adenoma of Patient 41751

source_name: Patient 41751


title: 43352: sessile serrated adenoma of Patient 41753

source_name: Patient 41753


title: 43394: sessile serrated adenoma of Patient 41755

source_name: Patient 41755


title: 43380: tubulovillous adenoma of Patient 41757

source_name: Patient 41757


title: 43383: tubulovillous adenoma of Patient 41758

source_name: Patient 41758


title: TH1 CD161_neg 4445 aCD2/3/28 6h


title: 43418: tubular adenoma of Patient 41761

source_name: Patient 41761


title: TH1 CD161_neg 4507 medium


title: 43366: tubular adenoma of Patient 41759

source_name: Patient 41759


title: PAOSX in LB, biological rep3

city: Evreux

first: Sylvie

last: Chevalier

address: 55, rue Saint Germain

department: Université de Rouen

institute: Normandie Université

hyb_protocol: Hybridizations were performed at the Mc Gill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca)

scan_protocol: Sacnning was done using a Genearray Scanner at the Mac Gill University and the Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca)

data_processing:
The data were analyzed with Flexarray 1.3 Software developped by Genome Quebec Innovation Centre at McGill University
Data were processed using the robust multiarray average algorithm (RMA) for normalization, background correction and expression value calculation

organism: Pseudomonas aeruginosa

source_name: PAOSX isogenic mutant strain

label_protocol: cDNA were synthetized, fragmented and labelled according to the standard affymetrix protocol for prokaryotic target from 10µg of RNA (GeneChip® Expression Analysis Technical Manual, affymetrix, P/N 702232 Rev. 3)

growth_protocol: Bacteria were grown overnight at 37°C on a rotary shaker (180 rpm) in mineral LB medium. Cultures were inoculated at an initial OD580 of 0.08 in fresh LB medium, and allowed to grow to mid log phase (OD580=0.7-0.8) before RNA extraction.

extract_protocol: RNA were extracted by the classical hot acid-phenol method.

value: PAOSX

tag: genotype/variation

value: sigX deletion mutant


title: TH1 CD161_neg 4404 aCD2/3/28 6h


title: TH1 CD161_neg 4507 aCD2/3/28 6h


title: PAOSX in LB, biological rep2


title: H103 in LB, biological rep3

source_name: wild type strain

value: Wild type strain


title: 43351: tubular adenoma of Patient 41756

source_name: Patient 41756


title: 43642: tubulovillous adenoma of Patient 41763

source_name: Patient 41763


title: Coculture, 100µM, Rep-3 [set 2]

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

description: US10293825_253949443443_S01_GE1_107_Sep09_2_2.txt:gProcessedSignal

hyb_protocol: Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volµMe of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: An Agilent Surescan Microarray Scanner (G2505 C, Agilent Technologies Inc.) was used to scan microarrays at 2 μm resolution.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data analysis was performed using GeneSpring version GX11.5 (Agilent Technologies) The TNT exposure experiments were analyzed individually.  Raw microarray data were first normalized to the 75th percentile within each array followed by median scaling among all exposures. The effects of the two main experimental conditions, culture (mono- versus co-culture) and chemical exposure level (DMSO+ control, dose 1 and dose 2), were tested for effects on  expression using two-way ANOVA where p = 0.01, including Benjamini-Hochberg multiple test corrections. Pairwise comparisons among experimental treatment levels were conducted using Welch unpaired unequal variance t-tests including a 1.5 fold cutoff. Finally, principal component analysis (PCA) was performed to visualize sµMmary-level trends in expression among treatments.

source_name: HK-2_Coculture_100µM TNT

label_protocol: The Agilent Low Input QuickAmp Labelling Kit protocol (Agilent Technologies) was utilized for cRNA synthesis with microarray hybridizations following manufacturer’s recommendations. Fifteen ng of total RNA was used for starting material and 600 ng of Cy3 labelled cRNA was used for hybridizations.

growth_protocol: Five cell lines (kidney proximal tubule epithelial cells: HK-2; liver: THLE-3; lung: NuLi-1; vascular endotheliµM: TeloHAEC; heart: AC10; all from American Type Culture Collection, ATCC®, Manassas, VA) derived from normal tissues were chosen for the broad representation of organ systems to maximize coverage of toxicity screening.  Cells were kept in an incubator at 37°C, 90% hµMidity and 5% CO2.  Culture vessels (25 and 75 cm2 tissue culture flasks) for liver, lung and heart muscle cells were coated with collagen as per manufacturer instructions (ATCC®, Manassas, VA).  Manufacturer recommended media and additives were used for each cell line.

extract_protocol: RNA from the mono- and co-culture cell samples was extracted using the NucleoSpin RNA XS kit (Clontech Laboratories Inc., Mountain View, CA, USA) following manufacturer instructions.  RNA quantity was assessed using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific Inc.).  RNA integrity was assessed through microelectrophoresis analysis using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany) run on an Agilent Bio-Analyzer (Agilent Technologies).  Only samples with RNA integrity nµMbers > 7 were used for the microarray hybridizations.

treatment_protocol: The IdMOC system is a 96-well plate divided into 16 chambers, each containing 6 wells that can be submerged with culture media in order to create a co-culture exposure.  For cells requiring a collagen coated surface (liver, lung and heart muscle cells), individual wells were coated with collagen/fibronectin as needed in advance of the addition of cells to the co-culture plate.  Each cell line was then placed in a well of an IdMOC chamber in its respective growth media as per manufacturer instructions within an initial monoculture exposure and then incubated for 24 hours.  After having confirmed that each cell line formed a confluent (80-95%) layer, cell line specific media was replaced by the pre-determined co-culture media (Universal Primary Cell Plating Media, In vitro ADMET Laboratories®), covering the entire set of wells.  Plates were then incubated on shakers at low speed for an additional 24 hours while exposed to the four exposure concentrations of TNT (plus controls) as determined by the cell viability assays described above where each treatment included four replicates.  Each 6 member well served as a statistical replicate in our IdMOC experiments.  Parallel to the co-culture exposures, monocultures in 96 well culture tissue plates were established using identical plating techniques, incubations, munitions exposure concentrations, and replication as described for the co-culture exposures to provide direct comparative testing of effects among the mono- and co-culture assays.  Upon exposure completion, all cells were then harvested, flash- frozen using liquid nitrogen and stored at -80°C.  The samples from the kidney cells exposed to the two highest concentrations of toxicants were selected for further investigation via transcript expression analysis in addition to kidney cells from the control exposures.  Kidney cells were selected due to the renal toxicity observed in mammalian TNT exposures (Levine et al. 1984, Dilley et al. 1982b, Levine et al. 1990b, US Army 1984a), and to test if potential TNT metabolism by liver cells in co-culture affected the overall toxicological response in kidney cells.

value: Kidney proximal tubule epithelial cells

tag: culture type

value: coculture

tag: exposed to

value: 100µM TNT


title: TH1 CD161_neg 4613 medium

source_name: human blood


title: TH1 CD161_neg 4404 medium


title: 43400: villous adenoma of Patient 41762

source_name: Patient 41762

value: villous adenoma


title: Coculture, 10µM, Rep-3 [set 2]

description: US10293825_253949443442_S01_GE1_107_Sep09_1_3.txt:gProcessedSignal

source_name: HK-2_Coculture_10µM TNT

value: 10µM TNT


title: Coculture, 100µM, Rep-1 [set 2]

description: US10293825_253949443385_S01_GE1_107_Sep09_2_4.txt:gProcessedSignal


title: Coculture, 10µM, Rep-4 [set 2]

description: US10293825_253949443385_S01_GE1_107_Sep09_2_3.txt:gProcessedSignal


title: Coculture, 100µM, Rep-2 [set 2]

description: US10293825_253949444910_S01_GE1_107_Sep09_2_3.txt:gProcessedSignal


title: Coculture, 100µM, Rep-4 [set 2]

description: US10293825_253949443443_S01_GE1_107_Sep09_2_3.txt:gProcessedSignal


title: H103 in LB, biological rep2


title: PAOSX in LB, biological rep1


title: 43697: tubulovillous adenoma of Patient 41764

source_name: Patient 41764

value: male


title: 43363: tubulovillous adenoma of Patient 41765

source_name: Patient 41765


title: 43429: tubulovillous adenoma of Patient 41766

source_name: Patient 41766


title: Coculture, 10µM, Rep-2 [set 2]

description: US10293825_253949444910_S01_GE1_107_Sep09_1_1.txt:gProcessedSignal


title: 43646: tubulovillous adenoma of Patient 41767

source_name: Patient 41767


title: Coculture, DMSO Control, Rep-4 [set 2]

description: US10293825_253949443385_S01_GE1_107_Sep09_1_1.txt:gProcessedSignal

source_name: HK-2_Coculture_DMSO Control

value: DMSO Control


title: 43637: tubulovillous adenoma of Patient 41768

source_name: Patient 41768


title: 43419: serrated adenoma of Patient 41770

source_name: Patient 41770


title: Coculture, DMSO Control, Rep-3 [set 2]

description: US10293825_253949443442_S01_GE1_107_Sep09_2_2.txt:gProcessedSignal


title: Coculture, 10µM, Rep-1 [set 2]

description: US10293825_253949444910_S01_GE1_107_Sep09_1_3.txt:gProcessedSignal


title: AZA016

city: La Jolla

first: Samuel

last: Danziger

address: 10300 Campus Point Dr

institute: Celgene

hyb_protocol: Performed according to manufacturer's instructions

data_processing: All data were processed using R (https://www.r-project.org/) and affy package from Bioconductor was used to compute the gene expression values based on RMA algorithm.

source_name: AML Cell Line

growth_protocol: AML193, HL60, KG1a, and HNT34 cells were cultured in RPMI SILAC media (Thermo FisherScientific; Waltham, MA) containing L-[12C6,14N2]lysine and L-[12C6,14N4]arginine (light label)

extract_protocol: Frozen cell pellets were harvested for DNA methylation (Infinium MethylationEPIC BeadChip, Illumina) and gene expression (GeneChip™ Human Genome U133 Plus 2.0 Array, Thermo Fisher Scientific) analyses

treatment_protocol: Cells were treated with vehicle (DMSO)or 0.5 μM AZA daily for 3 days. Cells were cultured for another 4 days in drug-free media

tag: drug treatment

value: 0.5uM AZA


title: 43632: serrated adenoma of Patient 41771

source_name: Patient 41771


title: TH1 CD161_neg 4445 medium

value: T Helper Lymphocyte 1


title: Coculture, DMSO Control, Rep-1 [set 2]

description: US10293825_253949443384_S01_GE1_107_Sep09_2_4.txt:gProcessedSignal

tag: cell line


title: Coculture, DMSO Control, Rep-2 [set 2]

description: US10293825_253949443385_S01_GE1_107_Sep09_1_2.txt:gProcessedSignal


title: AZA015

scan_protocol: Performed according to manufacturer's instructions


title: 43390: tubulovillous adenoma of Patient 41772

source_name: Patient 41772


title: AZA013

label_protocol: Performed according to manufacturer's instructions

value: vehicle


title: 2364B: Tumor of Patient 2364

source_name: Patient 2364

value: Male

value: Tumor

value: Invasive Adenocarcinoma

tag: tnm

value: pT1, pNX, pMX

tag: uicc

value: I


title: 2364A: Adenoma of Patient 2364

tag: age

tag: tissue

value: Adenoma

value: Adenovillous polyp


title: AZA014


title: 43402: tubular adenoma of Patient 41775

source_name: Patient 41775

tag: gender

value: female

value: colorectal adenoma

tag: adenomadiagnosis

value: tubular adenoma


title: Monoculture, 100µM, Rep-4 [set 2]

description: US10293825_253949443384_S01_GE1_107_Sep09_1_2.txt:gProcessedSignal

source_name: HK-2_Monoculture_100µM TNT

tag: cell type

value: Kidney proximal tubule epithelial cells

value: monoculture

value: 100µM TNT


title: DC maturation by LPS_4

city: seoul

first: Seong Hwi

last: Hong

address: 120 Neungdong-ro

department: School of Medicine

country: South Korea

institute: Konkuk University

description:
culture method: immature DCs were treated with 50 ng/ml LPS for O/N
Day7_4

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1. The file raw data.xlsx  includes gProcessed Signal for unique probes (no controls) and includes Flag data and probe annotation.

source_name: bone marrow progenitor cells

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: All cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol reagent, digested with DNase I and reverse transcribed using a High Capacity cDNA Reverse Transcription Kit

treatment_protocol: Immature DC cells were generated with monocytes treated with 10ng/ml GM-CSF and IL-4 for 6days. Mature DC cells were prepared by treatment with 50 ng/ml LPS for O/N on immature DCs.

value: mature DC

tag: cells derived from

value: bone marrow progenitor cells

tag: strain

tag: Sex


title: Monoculture, 100µM, Rep-2 [set 2]

description: US10293825_253949444909_S01_GE1_107_Sep09_2_4.txt:gProcessedSignal


title: AZA009


title: AZA011

value: 0.5uM AZA


title: AZA010

value: vehicle


title: 2942A: Adenoma of Patient 2942

source_name: Patient 2942

tag: patient id

value: Female

value: Villous Adenoma with Marked Dysplasia


title: 2364C: Adjacent Mucosa of Patient 2364

value: Male

value: Adjacent Mucosa

value: Benign


title: AZA012


title: AZA008


title: Monoculture, 100µM, Rep-3 [set 2]

description: US10293825_253949444910_S01_GE1_107_Sep09_2_1.txt:gProcessedSignal


title: DC maturation by LPS_3

description:
culture method: immature DCs were treated with 50 ng/ml LPS for O/N
Day7_3


title: 2942B: Tumor of Patient 2942

value: Tumor

value: Invasive Adenocarcinoma

value: pT3, pN0, pMX

value: IIA


title: AZA007


title: DC maturation by LPS_2

description:
culture method: immature DCs were treated with 50 ng/ml LPS for O/N
Day7_2

value: female


title: 2942C: Adjacent Mucosa of Patient 2942


title: AZA006


title: Monoculture, 10µM, Rep-2 [set 2]

description: US10293825_253949444910_S01_GE1_107_Sep09_2_2.txt:gProcessedSignal

source_name: HK-2_Monoculture_10µM TNT

value: Kidney proximal tubule epithelial cells

value: 10µM TNT


title: Monoculture, 100µM, Rep-1 [set 2]

description: US10293825_253949444909_S01_GE1_107_Sep09_1_2.txt:gProcessedSignal

value: monoculture

value: 100µM TNT


title: immature dendritic cells (DC) from bone marrow derived monocytes_4

description:
culture method: monocytes treated with 10ng/ml GM-CSF and IL-4 for 6days
Day6_4

value: immature dendritic cells (DC)

value: bone marrow progenitor cells


title: Monoculture, 10µM, Rep-3 [set 2]

description: US10293825_253949444909_S01_GE1_107_Sep09_1_1.txt:gProcessedSignal


title: Monoculture, 10µM, Rep-1 [set 2]

description: US10293825_253949443442_S01_GE1_107_Sep09_1_2.txt:gProcessedSignal


title: 3809A: Adenoma of Patient 3809

source_name: Patient 3809

value: Adenoma

value: Tubulovillous Adenoma


title: AZA005

value: vehicle


title: DC maturation by LPS_1

description:
culture method: immature DCs were treated with 50 ng/ml LPS for O/N
Day7_1

value: mature DC


title: immature dendritic cells (DC) from bone marrow derived monocytes_3

description:
culture method: monocytes treated with 10ng/ml GM-CSF and IL-4 for 6days
Day6_3


title: 3809B: Tumor of Patient 3809

value: Male

value: Infiltrating Adenocarcinoma


title: Monoculture, 10µM, Rep-4 [set 2]

description: US10293825_253949443443_S01_GE1_107_Sep09_1_1.txt:gProcessedSignal


title: AZA004

value: 0.5uM AZA


title: 3809C: Adjacent Mucosa of Patient 3809

value: Adjacent Mucosa

value: Benign


title: Monoculture, DMSO Control, Rep-3 [set 2]

description: US10293825_253949444909_S01_GE1_107_Sep09_1_4.txt:gProcessedSignal

source_name: HK-2_Monoculture_DMSO Control

value: DMSO Control


title: 3976A: Adenoma of Patient 3976

source_name: Patient 3976

value: Female


title: Monoculture, DMSO Control, Rep-2 [set 2]

description: US10293825_253949443443_S01_GE1_107_Sep09_1_3.txt:gProcessedSignal

value: Kidney proximal tubule epithelial cells


title: 3976B: Tumor of Patient 3976

value: Tumor

value: Colonic Adenocarcinoma

value: pT2, pN0, pMX

value: I


title: immature dendritic cells (DC) from bone marrow derived monocytes_1

description:
culture method: monocytes treated with 10ng/ml GM-CSF and IL-4 for 6days
Day6_1

value: immature dendritic cells (DC)

value: bone marrow progenitor cells

value: female


title: 3976C: Adjacent Mucosa of Patient 3976


title: immature dendritic cells (DC) from bone marrow derived monocytes_2

description:
culture method: monocytes treated with 10ng/ml GM-CSF and IL-4 for 6days
Day6_2


title: Monoculture, DMSO Control, Rep-1 [set 2]

description: US10293825_253949444909_S01_GE1_107_Sep09_2_2.txt:gProcessedSignal

value: monoculture


title: AZA003


title: AZA001

value: vehicle


title: NGFR_NS_A_2

hyb_protocol: Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix)

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software version 1.4 from Affymetrix.

data_processing: Data preprocessing was performed using R/Bioconductor (version 3.6) affy (version 1.56) package. Briefly, raw cel data was loaded into R and further normalized with the gcrma method. Statistical analysis and DE extraction were peformed with limma package (version 3.34.6).

source_name: Th17 cells

label_protocol: Labeling of total RNA to MG 430 GeneChips was performed using the whole-transcriptome pico KIT from Affymetrix according tot he manufacturer´s instruction.

growth_protocol: Cells were cultured in complete RPMI 1640 medium plus 100 IU/ml recombinant human IL-2

treatment_protocol: Cells were transduced with lentiviral vectors and then sorted by MACS technology to obtain almost 100% pure infected cell populations.

tag: transduction

value: Control-vector


title: Yap/Taz DKO ATII cell_infection_Day 8_1

city: Philadelphia

first: Ying

last: Tian

state: PA

address: 3500 N. Broad Street

department: Pharmacology, Center for Translational Medicine

institute: Lewis Katz School of Medicine at Temple University

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had a RMA expression value greater than the mean of the negative control probesets. Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available Gene Cluster 3.0 package (http://bonsai.hgc.jp/~mdehoon/software/cluster/).

source_name: Spc-Yap/Taz DKO ATII cells at day 8 post infection, 1

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

extract_protocol: RNA was extracted using Rneasy mini kit Q(Qiagene).

treatment_protocol: The mouse lineage-labelled ATII cells were harvested by FACS sorting GFP positive cells with or without bacterial infection.

tag: sample type

value: lung alveolar type II cell_Day 8 infection, male


title: Coculture, 1mM, Rep-3

description: US10293825_253949443443_S01_GE1_107_Sep09_1_2.txt:gProcessedSignal

hyb_protocol: Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data analysis was performed using GeneSpring version GX11.5 (Agilent Technologies) The DNAN exposure experiments were analyzed individually.  Raw microarray data were first normalized to the 75th percentile within each array followed by median scaling among all exposures. The effects of the two main experimental conditions, culture (mono- versus co-culture) and chemical exposure level (DMSO+ control, dose 1 and dose 2), were tested for effects on  expression using two-way ANOVA where p = 0.01, including Benjamini-Hochberg multiple test corrections. Pairwise comparisons among experimental treatment levels were conducted using Welch unpaired unequal variance t-tests including a 1.5 fold cutoff. Finally, principal component analysis (PCA) was performed to visualize summary-level trends in expression among treatments.

growth_protocol: Five cell lines (kidney proximal tubule epithelial cells: HK-2; liver: THLE-3; lung: NuLi-1; vascular endothelium: TeloHAEC; heart: AC10; all from American Type Culture Collection, ATCC®, Manassas, VA) derived from normal tissues were chosen for the broad representation of organ systems to maximize coverage of toxicity screening.  Cells were kept in an incubator at 37°C, 90% humidity and 5% CO2.  Culture vessels (25 and 75 cm2 tissue culture flasks) for liver, lung and heart muscle cells were coated with collagen as per manufacturer instructions (ATCC®, Manassas, VA).  Manufacturer recommended media and additives were used for each cell line.

extract_protocol: RNA from the mono- and co-culture cell samples was extracted using the NucleoSpin RNA XS kit (Clontech Laboratories Inc., Mountain View, CA, USA) following manufacturer instructions.  RNA quantity was assessed using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific Inc.).  RNA integrity was assessed through microelectrophoresis analysis using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany) run on an Agilent Bio-Analyzer (Agilent Technologies).  Only samples with RNA integrity numbers > 7 were used for the microarray hybridizations.

treatment_protocol: The IdMOC system is a 96-well plate divided into 16 chambers, each containing 6 wells that can be submerged with culture media in order to create a co-culture exposure.  For cells requiring a collagen coated surface (liver, lung and heart muscle cells), individual wells were coated with collagen/fibronectin as needed in advance of the addition of cells to the co-culture plate.  Each cell line was then placed in a well of an IdMOC chamber in its respective growth media as per manufacturer instructions within an initial monoculture exposure and then incubated for 24 hours.  After having confirmed that each cell line formed a confluent (80-95%) layer, cell line specific media was replaced by the pre-determined co-culture media (Universal Primary Cell Plating Media, In vitro ADMET Laboratories®), covering the entire set of wells.  Plates were then incubated on shakers at low speed for an additional 24 hours while exposed to the four exposure concentrations of DNAN (plus controls) as determined by the cell viability assays described above where each treatment included four replicates.  Each 6 member well served as a statistical replicate in our IdMOC experiments.  Parallel to the co-culture exposures, monocultures in 96 well culture tissue plates were established using identical plating techniques, incubations, munitions exposure concentrations, and replication as described for the co-culture exposures to provide direct comparative testing of effects among the mono- and co-culture assays.  Upon exposure completion, all cells were then harvested, flash- frozen using liquid nitrogen and stored at -80°C.  The samples from the kidney cells exposed to the two highest concentrations of toxicants were selected for further investigation via transcript expression analysis in addition to kidney cells from the control exposures.  Kidney cells were selected due to the renal toxicity observed in mammalian TNT exposures (Levine et al. 1984, Dilley et al. 1982b, Levine et al. 1990b, US Army 1984a), and to test if potential TNT metabolism by liver cells in co-culture affected the overall toxicological response in kidney cells.

tag: culture type

value: coculture

value: 1mM 2,4-dinitroanisole (DNAN)


title: Yap/Taz DKO ATII cell_infection_Day 8_2

source_name: Spc-Yap/Taz DKO ATII cells at day 8 post infection, 2


title: AZA002


title: Coculture, 1mM, Rep-2

description: US10293825_253949444910_S01_GE1_107_Sep09_1_4.txt:gProcessedSignal

tag: exposed to


title: 4397A: Adenoma of Patient 4397

data_processing: Data were analyzed using Bioconductor 3.2 running on R 3.2.2. Probeset expression measures were calculated using the Affymetrix package’s Robust Multichip Average (RMA) default method.

source_name: Patient 4397

extract_protocol: Qiagen RNAeasy FFPE

value: Adenoma

value: Tubulovillous Adenoma


title: Coculture, 1mM, Rep-4

description: US10293825_253949444909_S01_GE1_107_Sep09_2_3.txt:gProcessedSignal


title: 4397B: Tumor of Patient 4397

value: Female

value: pT3, pN1, pMX

value: IIIB


title: 4397C: Adjacent Mucosa of Patient 4397

value: Adjacent Mucosa

value: Benign


title: Coculture, 1mM, Rep-1

description: US10293825_253949443385_S01_GE1_107_Sep09_1_4.txt:gProcessedSignal

value: Kidney proximal tubule epithelial cells


title: EOMES_NS_A_2

value: Eomes-vector


title: NGFR_NS_A_1


title: 4755A: Adenoma of Patient 4755

source_name: Patient 4755

value: Tubulovillous Adenoma with Surface Atypia


title: Coculture, 100µM, Rep-4

description: US10293825_253949443442_S01_GE1_107_Sep09_2_4.txt:gProcessedSignal

value: 100µM 2,4-dinitroanisole (DNAN)


title: ATII cell_infection_Day 8

source_name: Spc-CreERT ATII cell at day 8 post infection


title: scrambled control, biological replicate 2

description: scrambled control-treated E18 primary hippocampus cells, biological replicate 2

hyb_protocol: 130µl hybridization mix prepared from labeled ssDNA was hybridized for 17h at 45°C to GeneChip Mouse Gene 2.0 ST arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_002.

data_processing: Data were preprocessed with the Expression Console v1.2.1.20 software (Affymetrix); background correction, nomalization and gene-level probeset summary were performed with the RMA sketch workflow using default parameter settings.

source_name: E18 primary hippocampus cells

label_protocol: 100ng of total RNA were amplified with the WT Expression Kit (Ambion), followed by ssDNA labeling with the WT Terminal Labeling Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: After dissection of hippocampi from mouse embryos at prenatal day 18, primary cell have been cultured in 6 well plates in Neurobasal medium with 2% B27 Supplement, 2mM L-Glutamine, 100 Units/ml Penicillin and 100µg/ml Streptomycin at 37°C.

extract_protocol: Total RNA was isolated 7 days after infection using the RNeasy Mini Plus Kit (Qiagen) according to manufacturers instructions.

treatment_protocol: Murine primary hippocampal cells have been infected with 4x10^9 AAV1/2 virus particles per well 7 days after seeding.

value: E18 primary hippocampus cells

tag: treatment

value: control

tag: rin


title: Coculture, 100µM, Rep-3

description: US10293825_253949443384_S01_GE1_107_Sep09_2_2.txt:gProcessedSignal

tag: cell line


title: scrambled control, biological replicate 3

description: scrambled control-treated E18 primary hippocampus cells, biological replicate 3


title: 4755B: Tumor of Patient 4755

value: Tumor

value: Infiltrating Adenocarcinoma

tag: tnm

value: pT2, pN0, pMX

tag: uicc

value: I


title: cFLIP, biological replica D

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

description: Gene expression data from c-FLIP-infected monocytes.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization. RMA data have been batch corrected using ComBat.

source_name: CD14+ cells isolated from buffy coat infected with FLIP-encoding lentivirus

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.

growth_protocol: Freshly-isolated human monocytes from buffy coats were infected for four hours by spin-inoculation and cultured for 18 hours in RPMI 10% FBS

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Human monocytes were infected with Luciferase- or c-FLIP- lentiviruses

value: in vitro infected monocytes from healthy donors

tag: infection

value: c-FLIP-infected


title: EOMES_NS_A_1


title: H1g

city: chengdu

first: qiang

middle: guo

last: zhu

state: sichuan

address: yihuanlu nanyiduan 24hao

country: China

institute: sichuan university

data_processing:
With Tophat v2.0.12 as a mapping tool, clean reads filtered out from raw reads were retained and mapped to the reference genome of Gallus gallus at ftp://ftp.ensembl.org/pub/release-72/fasta/gallus_gallus/dna.
HTSeq v0.6.1 was used to count the reads mapped to each gene. Due to the effect of sequencing depth and gene length for the reads count, FPKM was employed in present study as key parameter for the gene expression analyses.
Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by GOSeq Release2.12 and KOBAS v2.0 respectively.
Supplementary_files_format_and_content: FPKM

organism: Gallus gallus

source_name: granulose cell

extract_protocol:
Granulose cells were removed and frozen in RNAzol. the granulosa cells were isolated from 6 mm, F5 and F1 follicles on ice and dispersed in RNAzol reagent (Molecular Research Center, Cincinnati, OH, USA). The total RNAs were extracted according to the manufacturer’s instructions and dissolved in diethylpyrocarbonate-treated H2O.
RNA quantity and quality were assessed using a Nanodrop spectrophotometer and Agilent 2100 according to the manufacturer’s instructions. Briefly, the mRNA from total RNA (at least 3 μg) were enriched by poly-A oligo attached magnetic beads with an integrity value＞8.0. Double-stranded complementary DNAs were synthesized with random hexamer primers and purified with AMPure XP beads. The inserts with expected size were concentrated and subjected for the analyses.

value: natural granulosa cells in F1 follicle

tag: tissue

value: ovary

tag: age


title: Diras2 knockdown, biological replicate 3

description: Diras2 knockdown in E18 primary hippocampus cells, biological replicate 3

tag: cell type

value: Diras2 knockdown


title: ATII cell_no infection

source_name: Spc-CreERT ATII cell without infection

value: lung alveolar type II cell_no infection, male


title: Coculture, 100µM, Rep-2

description: US10293825_253949444910_S01_GE1_107_Sep09_1_2.txt:gProcessedSignal

value: coculture


title: 559A: Adenoma of Patient 559

city: Beerse

first: Joke

last: Reumers

address: Turnhoutseweg 32

institute: Janssen R&D

source_name: Patient 559

tag: gender

value: Male

value: Adenoma

tag: adenomadiagnosis

value: Tubulovillous Adenoma


title: scrambled control, biological replicate 1

description: scrambled control-treated E18 primary hippocampus cells, biological replicate 1


title: E5g

value: natural granulosa cells in F5 follicle


title: Coculture, 100µM, Rep-1

description: US10293825_253949443443_S01_GE1_107_Sep09_2_4.txt:gProcessedSignal

value: Kidney proximal tubule epithelial cells

value: 100µM 2,4-dinitroanisole (DNAN)


title: 4755C: Adjacent Mucosa of Patient 4755

value: Female

value: Adjacent Mucosa

value: Benign


title: cFLIP, biological replica B


title: H103 in LB, biological rep1

source_name: wild type strain

tag: strain

tag: genotype/variation

value: Wild type strain


title: A6g

value: natural granulosa cells in 6mm follicle


title: Diras2 knockdown, biological replicate 2

description: Diras2 knockdown in E18 primary hippocampus cells, biological replicate 2

value: E18 primary hippocampus cells


title: cFLIP, biological replica A

value: in vitro infected monocytes from healthy donors

value: c-FLIP-infected


title: Diras2 knockdown, biological replicate 1

description: Diras2 knockdown in E18 primary hippocampus cells, biological replicate 1

value: Diras2 knockdown


title: Coculture, DMSO Control, Rep-4

description: US10293825_253949444909_S01_GE1_107_Sep09_1_3.txt:gProcessedSignal

source_name: HK-2_Coculture_DMSO Control

value: DMSO Control


title: Coculture, DMSO Control, Rep-3

description: US10293825_253949443442_S01_GE1_107_Sep09_1_1.txt:gProcessedSignal

value: coculture


title: control, biological replicate F

description: Gene expression data from Luciferase-infected monocytes.

source_name: CD14+ cells isolated from buffy coat infected with luciferase-encoding lentivirus

value: Luciferase-infected


title: control, biological replicate G


title: 678A: Adenoma of Patient 678

source_name: Patient 678

tag: patient id

value: Male

value: Adenoma

value: Adenovillous Polyp


title: 559B: Tumor of Patient 559

value: Tumor

value: Infiltrating Adenocarcinoma

value: pT3, pN0, pMX

value: IIA


title: Coculture, DMSO Control, Rep-2

description: US10293825_253949443443_S01_GE1_107_Sep09_1_4.txt:gProcessedSignal

value: Kidney proximal tubule epithelial cells


title: Monoculture, 1mM, Rep-4

description: US10293825_253949443442_S01_GE1_107_Sep09_2_3.txt:gProcessedSignal

value: monoculture

value: 1mM 2,4-dinitroanisole (DNAN)


title: 678B: Tumor of Patient 678

value: Invasive Adenocarcinoma

value: pT2, pN0, pMX

value: I


title: control, biological replicate E

tag: sample type

value: in vitro infected monocytes from healthy donors


title: 1627A: Adenoma of Patient 1627

source_name: Patient 1627

value: Female

value: Tubular Adenoma


title: 678C: Adjacent Mucosa of Patient 678

value: Adjacent Mucosa

value: Benign


title: control, biological replicate D

value: Luciferase-infected


title: control, biological replicate C


title: Monoculture, 1mM, Rep-3

description: US10293825_253949443385_S01_GE1_107_Sep09_2_1.txt:gProcessedSignal

tag: culture type


title: 1627B: Tumor of Patient 1627

value: pT3, pN1, pMX

value: IIIB


title: Monoculture, 1mM, Rep-2

description: US10293825_253949443384_S01_GE1_107_Sep09_1_3.txt:gProcessedSignal

tag: exposed to


title: Monoculture, 100µM, Rep-4

description: US10293825_253949443385_S01_GE1_107_Sep09_1_3.txt:gProcessedSignal

value: 100µM 2,4-dinitroanisole (DNAN)


title: Coculture, DMSO Control, Rep-1

description: US10293825_253949443442_S01_GE1_107_Sep09_1_4.txt:gProcessedSignal

value: coculture

value: DMSO Control