title: scRNAseq, CGE E14.5 WT dissection

description:
AAACCTGCAATGGAAT-1  AAACCTGCAGCTGGCT-1  AAACCTGGTACCGTAT-1  AAACCTGGTTCCATGA-1  AAACCTGGTTGTGGAG-1  AAACCTGTCCAGAGGA-1  AAACCTGTCCCAACGG-1  AAACCTGTCTGTCCGT-1  AAACGGGAGGTGATTA-1  AAACGGGAGTAAGTAC-1  AAACGGGAGTCCTCCT-1  AAACGGGCACACGCTG-1  AAACGGGGTAAATGTG-1  AAACGGGGTTCTGGTA-1  AAACGGGGTTTGACTG-1  AAACGGGTCACTTATC-1  AAACGGGTCCGATATG-1  AAAGATGAGGCGCTCT-1  AAAGATGAGTAACCCT-1  AAAGATGAGTGCCAGA-1  AAAGATGCATCTATGG-1  AAAGATGGTGGTCTCG-1  AAAGATGTCACAAACC-1  AAAGCAAAGCAACGGT-1  AAAGCAAAGGATATAC-1  AAAGCAAAGTGTACCT-1  AAAGCAAAGTTCGCGC-1  AAAGCAACAACGATCT-1  AAAGCAACAACTGGCC-1  AAAGCAACAGATTGCT-1  AAAGCAACAGCCTGTG-1  AAAGCAAGTCCGAGTC-1  AAAGCAAGTTATCACG-1  AAAGCAATCACCAGGC-1  AAAGCAATCGCCAGCA-1  AAAGCAATCGGAAATA-1  AAAGCAATCGTAGGTT-1  AAAGTAGAGATCCGAG-1  AAAGTAGAGGTGCACA-1  AAAGTAGCAAGCCGTC-1  AAAGTAGCAAGTACCT-1  AAAGTAGGTAACGCGA-1  AAAGTAGGTACAAGTA-1  AAAGTAGGTCGTTGTA-1  AAAGTAGGTGATGTGG-1  AAAGTAGGTGGTACAG-1  AAAGTAGGTTCCATGA-1  AAATGCCAGGCCCGTT-1  AAATGCCAGTACGATA-1  AAATGCCCAAAGTCAA-1  AAATGCCGTAACGCGA-1  AAATGCCGTCCAAGTT-1  AAATGCCGTCCCTACT-1  AAATGCCGTGTTTGGT-1  AAATGCCTCGCCATAA-1  AAATGCCTCTTGTCAT-1  AACACGTCAAGTCTAC-1  AACACGTGTTAAGGGC-1  AACCATGAGCTATGCT-1  AACCATGCACATCTTT-1  AACCATGCACGAGGTA-1  AACCATGCAGGTCCAC-1  AACCATGGTCCGAATT-1  AACCATGGTTTGTGTG-1  AACCATGTCACCACCT-1  AACCATGTCGCATGAT-1  AACCGCGCAATCCGAT-1  AACCGCGCACGAAACG-1  AACCGCGGTACCGAGA-1  AACCGCGGTCAAAGAT-1  AACCGCGGTCCAGTTA-1  AACCGCGTCCAGATCA-1  AACCGCGTCGTAGATC-1  AACGTTGAGTGATCGG-1  AACGTTGCACCACCAG-1  AACGTTGCACGTTGGC-1  AACGTTGGTAATTGGA-1  AACGTTGGTGATGATA-1  AACGTTGGTGTCGCTG-1  AACGTTGGTGTGACCC-1  AACTCAGAGTGGTAAT-1  AACTCAGCAAACCTAC-1  AACTCAGCATGCTGGC-1  AACTCAGGTGTAACGG-1  AACTCAGGTTAAGACA-1  AACTCAGTCAACACTG-1  AACTCAGTCAAGCCTA-1  AACTCAGTCCTCGCAT-1  AACTCAGTCTCGTATT-1  AACTCCCCAAGAGGCT-1  AACTCCCCAGCATGAG-1  AACTCCCCATTAGCCA-1  AACTCCCGTGCTGTAT-1  AACTCCCTCTCAACTT-1  AACTCCCTCTGTACGA-1  AACTCTTAGCACCGTC-1  AACTCTTCACATGGGA-1  AACTCTTGTAACGTTC-1  AACTCTTGTAGGAGTC-1  AACTCTTTCCTCAACC-1  AACTCTTTCTCGTATT-1  AACTGGTCACTTAAGC-1  AACTGGTCAGTGGAGT-1  AACTGGTCATGAACCT-1  AACTGGTCATTCCTGC-1  AACTGGTGTACTCGCG-1  AACTGGTGTAGCGTCC-1  AACTGGTTCACATAGC-1  AACTGGTTCCATGAGT-1  AACTGGTTCTAAGCCA-1  AACTGGTTCTCCAGGG-1  AACTGGTTCTTGTCAT-1  AACTTTCAGCAACGGT-1  AACTTTCAGCTTCGCG-1  AACTTTCCAAGAGTCG-1  AACTTTCCATATACGC-1  AACTTTCCATTCGACA-1  AACTTTCGTAAACCTC-1  AACTTTCGTCCGTTAA-1  AACTTTCGTCTAACGT-1  AACTTTCGTCTTCAAG-1  AACTTTCGTTCGGCAC-1  AACTTTCTCAGCTGGC-1  AACTTTCTCCATGAGT-1  AAGACCTAGATGGGTC-1  AAGACCTAGGTAAACT-1  AAGACCTCACCGGAAA-1  AAGACCTCAGAAGCAC-1  AAGACCTCATATGGTC-1  AAGACCTCATCACGAT-1  AAGACCTCATGTCCTC-1  AAGACCTGTGGGTATG-1  AAGACCTGTGTTGAGG-1  AAGACCTGTTGTCGCG-1  AAGACCTTCCGTAGTA-1  AAGCCGCAGACTTTCG-1  AAGCCGCCAACGATGG-1  AAGCCGCCAGCTCGCA-1  AAGCCGCCATCAGTCA-1  AAGCCGCGTCACCCAG-1  AAGCCGCGTCACTTCC-1  AAGCCGCGTCTGCGGT-1  AAGCCGCGTTCCGTCT-1  AAGGAGCAGGGAAACA-1  AAGGAGCCACCAGATT-1  AAGGAGCCATGCTGGC-1  AAGGAGCTCAAAGTAG-1  AAGGCAGAGTGAAGTT-1  AAGGCAGCAATAACGA-1  AAGGCAGCATACGCCG-1  AAGGCAGGTCACTTCC-1  AAGGCAGGTCGGCACT-1  AAGGCAGTCGTACGGC-1  AAGGCAGTCTCAAACG-1  AAGGTTCAGATGCCTT-1  AAGTCTGAGTGGAGAA-1  AAGTCTGGTAAGGGCT-1  AAGTCTGTCAACCATG-1  AAGTCTGTCCGTCATC-1  AAGTCTGTCGGACAAG-1  AATCCAGAGACCCACC-1  AATCCAGAGCACACAG-1  AATCCAGAGGGTGTGT-1  AATCCAGCACGTCTCT-1  AATCCAGCAGAAGCAC-1  AATCCAGCAGGGTACA-1  AATCCAGCAGTATCTG-1  AATCCAGCATCCTTGC-1  AATCCAGGTCGTCTTC-1  AATCCAGTCCCGGATG-1  AATCCAGTCTACCAGA-1  AATCCAGTCTTGACGA-1  AATCGGTAGATGTGTA-1  AATCGGTAGCATCATC-1  AATCGGTAGCGTGAGT-1  AATCGGTAGCTACCTA-1  AATCGGTAGCTAGCCC-1  AATCGGTAGTCCTCCT-1  AATCGGTCAAGCGTAG-1  AATCGGTCAGCCAGAA-1  AATCGGTGTAGCGATG-1  AATCGGTGTAGCGCAA-1  AATCGGTGTTCCAACA-1  AATCGGTGTTCTGAAC-1  AATCGGTTCTAACCGA-1  AATCGGTTCTCGGACG-1  ACACCAAAGATCGATA-1  ACACCAAAGGACACCA-1  ACACCAAAGGCTACGA-1  ACACCAAAGTGTTTGC-1  ACACCAACAAGTACCT-1  ACACCAAGTCCGTCAG-1  ACACCAAGTCGCGTGT-1  ACACCAAGTCTAACGT-1  ACACCAATCGGTCTAA-1  ACACCCTAGAGTGACC-1  ACACCCTCAAGCGCTC-1  ACACCCTCAAGCTGGA-1  ACACCCTCACAGGCCT-1  ACACCCTCACCATGTA-1  ACACCCTCACCTCGTT-1  ACACCCTCAGCTCGCA-1  ACACCCTGTACAGCAG-1  ACACCCTGTGAGGGAG-1  ACACCCTTCATCTGTT-1  ACACCCTTCGATCCCT-1  ACACCCTTCGCCATAA-1  ACACCCTTCTGTGCAA-1  ACACCGGAGAGTTGGC-1  ACACCGGAGGCCATAG-1  ACACCGGCACAGGAGT-1  ACACCGGCAGTCCTTC-1  ACACCGGGTAAATGAC-1  ACACCGGGTCGTCTTC-1  ACACCGGGTGGTAACG-1  ACACCGGTCACAAACC-1  ACACCGGTCGCCAAAT-1  ACACCGGTCGGTGTTA-1  ACACCGGTCTAACTTC-1  ACACCGGTCTCGAGTA-1  ACACTGAAGTGTCCAT-1  ACACTGACAGACAAAT-1  ACACTGACAGATGAGC-1  ACACTGACAGCCTGTG-1  ACACTGAGTACCTACA-1  ACACTGAGTCCTCTTG-1  ACACTGAGTCGGCATC-1  ACACTGATCACGCGGT-1  ACACTGATCAGTTCGA-1  ACACTGATCGTGGGAA-1  ACAGCCGAGAACTGTA-1  ACAGCCGAGCCACGTC-1  ACAGCCGCAAGCCGCT-1  ACAGCCGCATCAGTAC-1  ACAGCCGCATCTATGG-1  ACAGCCGCATGCCTTC-1  ACAGCCGTCACTTACT-1  ACAGCCGTCACTTATC-1  ACAGCCGTCAGTTAGC-1  ACAGCTAAGCCGCCTA-1  ACAGCTAAGCGATATA-1  ACAGCTAGTAGTAGTA-1  ACAGCTAGTCCGAACC-1  ACAGCTAGTGACAAAT-1  ACAGCTAGTGCCTGTG-1  ACAGCTAGTTTGACTG-1  ACAGCTATCCGCATAA-1  ACAGCTATCGACAGCC-1  ACATACGAGAATCTCC-1  ACATACGAGATAGTCA-1  ACATACGAGCAAATCA-1  ACATACGAGTGAATTG-1  ACATACGAGTGGCACA-1  ACATACGCAAGTTGTC-1  ACATACGCACAGGTTT-1  ACATACGCAGAGTGTG-1  ACATACGCAGCTCCGA-1  ACATACGTCTGATTCT-1  ACATCAGAGATGTGGC-1  ACATCAGCACGAAAGC-1  ACATCAGGTCAGAAGC-1  ACATCAGGTCTTCTCG-1  ACATCAGGTGCAGACA-1  ACATCAGGTTAAGAAC-1  ACATCAGGTTCACCTC-1  ACATCAGTCACTGGGC-1  ACATCAGTCGCGCCAA-1  ACATGGTAGCGTTTAC-1  ACATGGTAGCTCAACT-1  ACATGGTAGGAGTTGC-1  ACATGGTCAAATCCGT-1  ACATGGTCAAGCCTAT-1  ACATGGTCAAGGTTCT-1  ACATGGTCACAAGACG-1  ACATGGTCACACGCTG-1  ACATGGTCAGGGTTAG-1  ACATGGTGTCGCGTGT-1  ACATGGTTCGTGACAT-1  ACATGGTTCTCTAGGA-1  ACATGGTTCTGCTTGC-1  ACCAGTAAGCCAGAAC-1  ACCAGTAAGCTAACAA-1  ACCAGTACACTGAAGG-1  ACCAGTAGTCATGCAT-1  ACCAGTAGTCCGAAGA-1  ACCAGTATCGAATGCT-1  ACCCACTAGACATAAC-1  ACCCACTAGCGCCTCA-1  ACCCACTAGGACACCA-1  ACCCACTAGTACGATA-1  ACCCACTAGTATTGGA-1  ACCCACTCAACACCCG-1  ACCCACTCATGGGACA-1  ACCCACTGTAAGTGTA-1  ACCCACTGTGATGATA-1  ACCCACTTCTACTCAT-1  ACCGTAAAGAAGAAGC-1  ACCGTAAAGGAGCGTT-1  ACCGTAAAGGCCCGTT-1  ACCGTAAAGGGCTTGA-1  ACCGTAAAGTACATGA-1  ACCGTAACATGTTCCC-1  ACCTTTAAGCTGAAAT-1  ACCTTTACACCGAAAG-1  ACCTTTACAGTCCTTC-1  ACCTTTACATACGCTA-1  ACCTTTACATGGGAAC-1  ACCTTTAGTCGGGTCT-1  ACCTTTAGTGTTGGGA-1  ACCTTTAGTTGATTCG-1  ACCTTTATCGCGGATC-1  ACCTTTATCGTGACAT-1  ACGAGCCAGAGTACAT-1  ACGAGCCAGATAGGAG-1  ACGAGCCAGGAATCGC-1  ACGAGCCAGGGAACGG-1  ACGAGCCAGTAATCCC-1  ACGAGCCCACATGGGA-1  ACGAGCCGTAGGAGTC-1  ACGAGCCGTTACGCGC-1  ACGAGCCTCCTTTCTC-1  ACGAGCCTCTTGCATT-1  ACGAGCCTCTTTACAC-1  ACGAGGAAGAATCTCC-1  ACGAGGAAGTAACCCT-1  ACGAGGACAAGACGTG-1  ACGAGGAGTAGAGGAA-1  ACGAGGAGTCGAACAG-1  ACGAGGATCAGTTTGG-1  ACGAGGATCATGTCTT-1  ACGATACAGGTTCCTA-1  ACGATACGTCCCTTGT-1  ACGATACTCTCGATGA-1  ACGATGTAGTCGAGTG-1  ACGATGTCAATAGCAA-1  ACGATGTCAGAGCCAA-1  ACGATGTGTCTAGCGC-1  ACGATGTTCGGTGTTA-1  ACGATGTTCTCCCTGA-1  ACGCAGCAGAGGTTGC-1  ACGCAGCAGGCAAAGA-1  ACGCAGCAGTACGCCC-1  ACGCAGCAGTGAACGC-1  ACGCAGCCAGCGTCCA-1  ACGCAGCCATAAGACA-1  ACGCAGCTCCACGCAG-1  ACGCAGCTCCATGAGT-1  ACGCAGCTCCCTCAGT-1  ACGCAGCTCCTTTCGG-1  ACGCCAGAGCAAATCA-1  ACGCCAGCACGTGAGA-1  ACGCCAGCATGACATC-1  ACGCCAGGTAAACACA-1  ACGCCAGGTATATGAG-1  ACGCCAGTCATCGGAT-1  ACGCCAGTCTCCTATA-1  ACGCCGAAGACTTTCG-1  ACGCCGAAGAGGGATA-1  ACGCCGAAGCAGCCTC-1  ACGCCGAAGGCCCGTT-1  ACGCCGAAGTTAGGTA-1  ACGCCGACAATAGCGG-1  ACGCCGACACGAAAGC-1  ACGCCGACATATACGC-1  ACGCCGAGTCAGCTAT-1  ACGCCGATCACCTTAT-1  ACGCCGATCGTACCGG-1  ACGCCGATCGTTACGA-1  ACGCCGATCTTGTATC-1  ACGGAGAAGACTTGAA-1  ACGGAGACACATTTCT-1  ACGGAGACAGTGGAGT-1  ACGGAGACATGCCCGA-1  ACGGAGACATTACGAC-1  ACGGAGAGTGATGTCT-1  ACGGAGATCAAGAAGT-1  ACGGAGATCCCTCTTT-1  ACGGAGATCCGTAGGC-1  ACGGAGATCGTCCAGG-1  ACGGAGATCTTGTTTG-1  ACGGCCAAGCAATATG-1  ACGGCCAAGCGATTCT-1  ACGGCCAAGGCAAAGA-1  ACGGCCACACAGACTT-1  ACGGCCAGTACCGGCT-1  ACGGCCAGTAGCGTGA-1  ACGGCCAGTGCCTTGG-1  ACGGCCATCACGGTTA-1  ACGGCCATCCGAATGT-1  ACGGCCATCCGCAAGC-1  ACGGCCATCCTCATTA-1  ACGGCCATCCTTGACC-1  ACGGGCTAGTGGTCCC-1  ACGGGCTCAACTGCTA-1  ACGGGCTCAATGAAAC-1  ACGGGCTCAATGTTGC-1  ACGGGCTGTAAAGTCA-1  ACGGGCTGTGGGTCAA-1  ACGGGCTTCAAGATCC-1  ACGGGTCAGCTAGTGG-1  ACGGGTCAGGCAAAGA-1  ACGGGTCAGGGATACC-1  ACGGGTCAGTTGCAGG-1  ACGGGTCCAATCACAC-1  ACGGGTCCACGCCAGT-1  ACGGGTCCAGCGTCCA-1  ACGGGTCCATGACGGA-1  ACGGGTCTCACCGGGT-1  ACGGGTCTCATCACCC-1  ACGTCAAGTAAATGTG-1  ACGTCAAGTACATGTC-1  ACGTCAAGTACCGTAT-1  ACGTCAAGTCCCTACT-1  ACGTCAATCACTCCTG-1  ACGTCAATCAGGATCT-1  ACTATCTCAAGGACTG-1  ACTATCTCAAGTACCT-1  ACTATCTCACAGGTTT-1  ACTATCTCAGCTGTTA-1  ACTATCTCATCTATGG-1  ACTATCTCATTTGCTT-1  ACTATCTGTCATACTG-1  ACTATCTGTCTAGGTT-1  ACTATCTGTGAAAGAG-1  ACTATCTTCACTATTC-1  ACTATCTTCAGCTGGC-1  ACTGAACAGAGCAATT-1  ACTGAACAGCACCGTC-1  ACTGAACAGCGATAGC-1  ACTGAACAGGCTCTTA-1  ACTGAACAGTGTGAAT-1  ACTGAACCAATAACGA-1  ACTGAACCACCGAATT-1  ACTGAACCACTAGTAC-1  ACTGAACCAGCATGAG-1  ACTGAACCAGCTGTGC-1  ACTGAACCAGTCACTA-1  ACTGAACGTATAAACG-1  ACTGAACGTCAGAAGC-1  ACTGAACGTTAGAACA-1  ACTGAACGTTCAGTAC-1  ACTGAGTAGAGCTGCA-1  ACTGAGTCATGCAACT-1  ACTGAGTGTCATGCCG-1  ACTGAGTGTCTAAAGA-1  ACTGAGTGTGATAAAC-1  ACTGAGTGTGCTCTTC-1  ACTGAGTGTGTCGCTG-1  ACTGAGTTCACCGGGT-1  ACTGAGTTCTTTACAC-1  ACTGATGAGAAACCTA-1  ACTGATGAGAATCTCC-1  ACTGATGCAAGTTAAG-1  ACTGATGCACAACGCC-1  ACTGATGCACGCGAAA-1  ACTGATGCAGCCTTGG-1  ACTGATGCAGCGTTCG-1  ACTGATGGTACAAGTA-1  ACTGATGGTGACTCAT-1  ACTGATGTCGGTTCGG-1  ACTGATGTCGTAGGAG-1  ACTGATGTCTGGGCCA-1  ACTGATGTCTGTCTCG-1  ACTGATGTCTTGTATC-1  ACTGCTCAGCGTTCCG-1  ACTGCTCAGTAGGTGC-1  ACTGCTCAGTGCTGCC-1  ACTGCTCCAGTAACGG-1  ACTGCTCGTCTGCAAT-1  ACTGCTCGTTCAGGCC-1  ACTGCTCTCTATCCCG-1  ACTGTCCAGCATCATC-1  ACTGTCCAGCCACCTG-1  ACTGTCCAGCTGATAA-1  ACTGTCCAGCTGTTCA-1  ACTGTCCAGGCTAGCA-1  ACTGTCCCACGCATCG-1  ACTGTCCCATGATCCA-1  ACTGTCCGTGATGTGG-1  ACTGTCCGTGCTTCTC-1  ACTGTCCGTTACAGAA-1  ACTGTCCGTTCCTCCA-1  ACTGTCCTCGCCGTGA-1  ACTGTCCTCTGAGTGT-1  ACTTACTAGATCCTGT-1  ACTTACTAGCCTTGAT-1  ACTTACTAGGCATGTG-1  ACTTACTCACAGCGTC-1  ACTTACTCATTGGTAC-1  ACTTACTGTAAACCTC-1  ACTTACTGTGCAACTT-1  ACTTACTGTGTTCGAT-1  ACTTACTTCAACGCTA-1  ACTTACTTCAGTTAGC-1  ACTTGTTAGAACAATC-1  ACTTGTTAGACAGAGA-1  ACTTGTTAGGTTACCT-1  ACTTGTTAGTGGTCCC-1  ACTTGTTAGTGTCTCA-1  ACTTGTTCAAACTGTC-1  ACTTGTTCACCCATGG-1  ACTTGTTCACGTTGGC-1  ACTTGTTCATTAACCG-1  ACTTGTTGTAAGTGGC-1  ACTTGTTGTACCATCA-1  ACTTGTTTCACGCATA-1  ACTTGTTTCGTCCGTT-1  ACTTGTTTCTGTCTCG-1  ACTTGTTTCTTGCCGT-1  ACTTTCAAGACAGGCT-1  ACTTTCAAGACTTGAA-1  ACTTTCACAATGAATG-1  ACTTTCAGTCATACTG-1  ACTTTCAGTCTGCCAG-1  AGAATAGAGAGGACGG-1  AGAATAGAGGGAGTAA-1  AGAATAGCATCTATGG-1  AGAATAGGTAGCCTCG-1  AGAATAGGTGCAGGTA-1  AGAATAGGTTCGGGCT-1  AGAATAGGTTTGACAC-1  AGAATAGTCCACGTTC-1  AGAATAGTCTCGCATC-1  AGACGTTAGCAAATCA-1  AGACGTTAGCCATCGC-1  AGACGTTAGGCCGAAT-1  AGACGTTAGTTCGCGC-1  AGACGTTCAAACTGCT-1  AGACGTTCAAGCTGGA-1  AGACGTTCAATCGAAA-1  AGACGTTCAATCGGTT-1  AGACGTTCACATTTCT-1  AGACGTTCAGTAAGCG-1  AGACGTTCATCAGTAC-1  AGACGTTCATCCTAGA-1  AGACGTTCATGCATGT-1  AGACGTTGTCTGATCA-1  AGACGTTGTTATTCTC-1  AGACGTTTCCTTTCTC-1  AGACGTTTCTAACTGG-1  AGACGTTTCTCTGCTG-1  AGACGTTTCTTGAGGT-1  AGAGCGAAGGGATGGG-1  AGAGCGACACGGTAGA-1  AGAGCGACAGACAAGC-1  AGAGCGACATCTCCCA-1  AGAGCGAGTCCAAGTT-1  AGAGCGAGTCCTGCTT-1  AGAGCGAGTGAGCGAT-1  AGAGCGATCATGGTCA-1  AGAGCGATCGCCAAAT-1  AGAGCGATCTAGAGTC-1  AGAGCGATCTCTTATG-1  AGAGCTTAGCCTTGAT-1  AGAGCTTAGCTAGTCT-1  AGAGCTTAGTCATCCA-1  AGAGCTTCACCAACCG-1  AGAGCTTCAGTAAGCG-1  AGAGCTTGTAGCCTAT-1  AGAGCTTGTATGAATG-1  AGAGCTTTCACCTCGT-1  AGAGCTTTCCACGACG-1  AGAGCTTTCGGTGTTA-1  AGAGCTTTCTACTATC-1  AGAGTGGAGAGCCCAA-1  AGAGTGGAGAGTGAGA-1  AGAGTGGAGCAGGCTA-1  AGAGTGGAGCGGCTTC-1  AGAGTGGAGCGTAATA-1  AGAGTGGAGCTGCGAA-1  AGAGTGGCAGGATCGA-1  AGAGTGGCAGGGTTAG-1  AGAGTGGTCGAACGGA-1  AGAGTGGTCGGAAATA-1  AGAGTGGTCGGTCTAA-1  AGAGTGGTCTTGCCGT-1  AGATCTGAGCCAGAAC-1  AGATCTGCACATGACT-1  AGATCTGCACCTATCC-1  AGATCTGCACGGTAGA-1  AGATCTGCAGCGATCC-1  AGATCTGCATGCCCGA-1  AGATCTGGTAGCAAAT-1  AGATCTGGTTGATTGC-1  AGATCTGTCACCATAG-1  AGATCTGTCTCCAACC-1  AGATTGCAGTAGGTGC-1  AGATTGCAGTGGGCTA-1  AGATTGCCAACACCTA-1  AGATTGCGTAATTGGA-1  AGATTGCGTTATCACG-1  AGATTGCTCGGAATCT-1  AGCAGCCAGAATCTCC-1  AGCAGCCAGAGACGAA-1  AGCAGCCAGGCCATAG-1  AGCAGCCAGGCTCTTA-1  AGCAGCCGTAAAGTCA-1  AGCAGCCGTAAGGGAA-1  AGCAGCCGTAAGGGCT-1  AGCAGCCGTGTAATGA-1  AGCAGCCTCCGCAGTG-1  AGCAGCCTCGCGTTTC-1  AGCAGCCTCTCTTATG-1  AGCATACAGACTACAA-1  AGCATACAGACTGGGT-1  AGCATACAGAGCCTAG-1  AGCATACAGTCATCCA-1  AGCATACAGTGCCATT-1  AGCATACCAATGGACG-1  AGCATACCACATTTCT-1  AGCATACGTATATGAG-1  AGCATACGTTGGACCC-1  AGCATACTCCGTCATC-1  AGCCTAAAGAGATGAG-1  AGCCTAAAGATCGATA-1  AGCCTAACAGGTGCCT-1  AGCCTAACATCCGCGA-1  AGCCTAAGTTGTCGCG-1  AGCCTAATCCGAACGC-1  AGCCTAATCTCTTATG-1  AGCCTAATCTTTCCTC-1  AGCGGTCAGAACAATC-1  AGCGGTCAGCGCTTAT-1  AGCGGTCAGCTGGAAC-1  AGCGGTCAGGGATGGG-1  AGCGGTCCACGCATCG-1  AGCGGTCGTTATCACG-1  AGCGGTCTCAGAAATG-1  AGCGTATAGATCTGAA-1  AGCGTATAGTGAACAT-1  AGCGTATCAGATCTGT-1  AGCGTATGTCATGCAT-1  AGCGTATGTCCATGAT-1  AGCGTATTCTCTAGGA-1  AGCGTATTCTTGAGGT-1  AGCGTCGCATTCCTCG-1  AGCGTCGGTACTCGCG-1  AGCGTCGGTGCGATAG-1  AGCGTCGGTTGACGTT-1  AGCGTCGGTTGGTTTG-1  AGCGTCGTCAACGAAA-1  AGCTCCTAGCCAGAAC-1  AGCTCCTAGGCTAGGT-1  AGCTCCTAGTAGATGT-1  AGCTCCTAGTCCATAC-1  AGCTCCTAGTGTCTCA-1  AGCTCCTCATCGGAAG-1  AGCTCCTGTATAAACG-1  AGCTCCTTCGGATGGA-1  AGCTCCTTCGTAGGTT-1  AGCTCCTTCGTCGTTC-1  AGCTCCTTCTCCAACC-1  AGCTCCTTCTCTGTCG-1  AGCTCTCAGAGATGAG-1  AGCTCTCCAAGCCATT-1  AGCTCTCCACGTCAGC-1  AGCTCTCGTAATCACC-1  AGCTCTCGTCAACTGT-1  AGCTCTCGTGTAACGG-1  AGCTCTCGTTAAAGAC-1  AGCTCTCGTTGTGGAG-1  AGCTCTCTCAAGATCC-1  AGCTCTCTCCCAAGAT-1  AGCTCTCTCCTGCAGG-1  AGCTCTCTCCTGTAGA-1  AGCTCTCTCTCGTATT-1  AGCTCTCTCTCGTTTA-1  AGCTTGAAGCGTAATA-1  AGCTTGACAAGTCTAC-1  AGCTTGACAATAAGCA-1  AGCTTGACACCTCGGA-1  AGCTTGAGTCTTCAAG-1  AGCTTGAGTCTTTCAT-1  AGCTTGAGTTAAAGTG-1  AGCTTGAGTTCAGGCC-1  AGCTTGATCGGAAACG-1  AGCTTGATCGTTGCCT-1  AGGCCACAGAGCCCAA-1  AGGCCACAGCGGCTTC-1  AGGCCACAGCTGAAAT-1  AGGCCACCAAGAAAGG-1  AGGCCACCAATGACCT-1  AGGCCACCACCAGGTC-1  AGGCCACCATCCAACA-1  AGGCCACGTAGGACAC-1  AGGCCACTCACAACGT-1  AGGCCACTCAGAGGTG-1  AGGCCACTCTTGCCGT-1  AGGCCGTAGACATAAC-1  AGGCCGTAGGGATACC-1  AGGCCGTAGGGATGGG-1  AGGCCGTCACCAGTTA-1  AGGCCGTCATTGGCGC-1  AGGCCGTGTAAACGCG-1  AGGCCGTGTACCGCTG-1  AGGCCGTGTCCAGTTA-1  AGGCCGTTCAGAAATG-1  AGGCCGTTCATGTAGC-1  AGGGAGTAGGCTCATT-1  AGGGAGTAGTACGACG-1  AGGGAGTAGTACGTTC-1  AGGGAGTAGTTCGCAT-1  AGGGAGTCAAGCCATT-1  AGGGAGTCAGGATCGA-1  AGGGAGTCATCCGTGG-1  AGGGAGTGTAAAGTCA-1  AGGGAGTGTAATTGGA-1  AGGGAGTGTACCGTTA-1  AGGGAGTTCACAGTAC-1  AGGGAGTTCACTATTC-1  AGGGAGTTCATGCTCC-1  AGGGATGAGCTGATAA-1  AGGGATGAGGTAGCCA-1  AGGGATGAGGTGTGGT-1  AGGGATGAGTGGGCTA-1  AGGGATGCAAGTTGTC-1  AGGGATGCACACCGCA-1  AGGGATGCACGCCAGT-1  AGGGATGCAGCATACT-1  AGGGATGCAGTTAACC-1  AGGGATGGTGTGGTTT-1  AGGGATGTCCACGCAG-1  AGGGATGTCCTTAATC-1  AGGGATGTCGCGTTTC-1  AGGGTGAAGAAGGTGA-1  AGGGTGAAGCCACTAT-1  AGGGTGACACGCATCG-1  AGGGTGACAGACAGGT-1  AGGGTGACAGGGTTAG-1  AGGGTGACAGGTGCCT-1  AGGGTGACATGTCTCC-1  AGGGTGAGTGCCTTGG-1  AGGGTGAGTGTATGGG-1  AGGGTGAGTTCAGGCC-1  AGGGTGAGTTGTGGCC-1  AGGGTGATCCTTTACA-1  AGGTCATAGCGATAGC-1  AGGTCATAGCTGAAAT-1  AGGTCATAGGAGTTTA-1  AGGTCATAGTGGGATC-1  AGGTCATCAGTAAGCG-1  AGGTCATCATGGTTGT-1  AGGTCATGTAATTGGA-1  AGGTCATGTATAGTAG-1  AGGTCATGTCAACTGT-1  AGGTCATGTTAAAGTG-1  AGGTCATGTTACAGAA-1  AGGTCATTCTGCCAGG-1  AGGTCCGCAAGCGAGT-1  AGGTCCGGTCTAAACC-1  AGTAGTCAGCTGGAAC-1  AGTAGTCCAAGCCATT-1  AGTAGTCCACCATGTA-1  AGTAGTCCACCCTATC-1  AGTAGTCCATAAGACA-1  AGTAGTCCATCCGGGT-1  AGTAGTCGTCCTAGCG-1  AGTAGTCGTGATAAGT-1  AGTAGTCGTTACGGAG-1  AGTAGTCTCAATACCG-1  AGTAGTCTCAGTTTGG-1  AGTAGTCTCCTAGGGC-1  AGTAGTCTCGAGCCCA-1  AGTCTTTAGCTAGTGG-1  AGTCTTTAGGAATGGA-1  AGTCTTTAGTGCAAGC-1  AGTCTTTCAAAGTCAA-1  AGTCTTTCAAGCCGTC-1  AGTCTTTTCGAATGGG-1  AGTCTTTTCGGAAATA-1  AGTGAGGAGACCCACC-1  AGTGAGGCAGTCAGCC-1  AGTGAGGCAGTCCTTC-1  AGTGAGGCATTCTTAC-1  AGTGAGGGTATAGGTA-1  AGTGAGGGTCCAACTA-1  AGTGAGGGTCTGGAGA-1  AGTGAGGGTTCAGACT-1  AGTGAGGGTTGTCTTT-1  AGTGAGGTCACGGTTA-1  AGTGAGGTCCCTTGCA-1  AGTGAGGTCGTCGTTC-1  AGTGGGAAGAGCTTCT-1  AGTGGGAAGCGTTGCC-1  AGTGGGACAGGATCGA-1  AGTGGGACATCACGTA-1  AGTGGGAGTCTAGTCA-1  AGTGGGAGTCTCCCTA-1  AGTGGGAGTGCACGAA-1  AGTGGGAGTGCTCTTC-1  AGTGGGATCAGGATCT-1  AGTGTCAAGCGACGTA-1  AGTGTCAAGGAATGGA-1  AGTGTCACATACAGCT-1  AGTGTCAGTAAGTGTA-1  AGTGTCAGTATATGAG-1  AGTGTCAGTGAGGCTA-1  AGTGTCAGTGAGGGAG-1  AGTGTCAGTTCCACTC-1  AGTGTCATCGCAAGCC-1  AGTGTCATCTGAAAGA-1  AGTTGGTAGGATGGAA-1  AGTTGGTGTACGCACC-1  AGTTGGTGTAGAGTGC-1  AGTTGGTGTCATATCG-1  AGTTGGTGTCTGGAGA-1  AGTTGGTTCTCGTTTA-1  ATAACGCAGAGGTTGC-1  ATAACGCAGGCTCATT-1  ATAACGCCAACTGCTA-1  ATAACGCCAAGCGAGT-1  ATAACGCTCAGGTTCA-1  ATAACGCTCGGAATCT-1  ATAAGAGAGAACAACT-1  ATAAGAGAGACATAAC-1  ATAAGAGAGATGCCAG-1  ATAAGAGAGGGTTCCC-1  ATAAGAGCAAGCTGGA-1  ATAAGAGCAGAAGCAC-1  ATAAGAGCAGGAACGT-1  ATAAGAGCAGGTTTCA-1  ATAAGAGGTACCATCA-1  ATAAGAGGTATAGTAG-1  ATAAGAGGTATATCCG-1  ATAAGAGGTGCCTTGG-1  ATAAGAGGTGTATGGG-1  ATAAGAGTCATTGCGA-1  ATAAGAGTCGCGTAGC-1  ATAAGAGTCGGTCCGA-1  ATAAGAGTCTACCAGA-1  ATAGACCAGAGGTTAT-1  ATAGACCCACCCATTC-1  ATAGACCCAGTCAGAG-1  ATAGACCGTAATCACC-1  ATAGACCGTATATGGA-1  ATAGACCGTCCGAGTC-1  ATAGACCTCAAAGACA-1  ATAGACCTCACATGCA-1  ATCACGAAGGCATTGG-1  ATCACGAAGTGAAGAG-1  ATCACGACAATGTAAG-1  ATCACGACACCACCAG-1  ATCACGAGTCCGAACC-1  ATCACGAGTCTCATCC-1  ATCACGATCTCCAACC-1  ATCATCTCAAGGTGTG-1  ATCATCTCACCTATCC-1  ATCATCTCATTCTCAT-1  ATCATCTGTAGCGTCC-1  ATCATCTGTAGCGTGA-1  ATCATCTGTTAGGGTG-1  ATCATCTGTTCAGTAC-1  ATCATCTTCGCGCCAA-1  ATCATCTTCGCGTTTC-1  ATCATCTTCTGTCTCG-1  ATCATGGAGCAGCGTA-1  ATCATGGAGGCTCTTA-1  ATCATGGCAGACACTT-1  ATCATGGCAGCCACCA-1  ATCATGGGTAGAGGAA-1  ATCATGGGTCCGTTAA-1  ATCATGGGTGCCTGGT-1  ATCATGGGTGTTAAGA-1  ATCATGGGTTATGCGT-1  ATCATGGTCTCATTCA-1  ATCATGGTCTGCTGTC-1  ATCCACCAGGACACCA-1  ATCCACCCAACACGCC-1  ATCCACCCACGAGAGT-1  ATCCACCCAGGTCGTC-1  ATCCACCGTAAAGGAG-1  ATCCACCGTCGACTGC-1  ATCCACCTCTTTAGGG-1  ATCCGAAAGAGAGCTC-1  ATCCGAACACAGATTC-1  ATCCGAACACCGCTAG-1  ATCCGAACAGCGTAAG-1  ATCCGAAGTCTCCACT-1  ATCCGAAGTGCAGGTA-1  ATCCGAATCCGAAGAG-1  ATCGAGTAGCTTATCG-1  ATCGAGTGTGCTAGCC-1  ATCGAGTTCCACGTGG-1  ATCTACTCAAGCCTAT-1  ATCTACTGTCTAGTCA-1  ATCTACTTCATCACCC-1  ATCTACTTCGAGAACG-1  ATCTACTTCTTGTTTG-1  ATCTGCCAGAAAGTGG-1  ATCTGCCAGTCTCCTC-1  ATCTGCCCAGACGTAG-1  ATCTGCCCAGTCGATT-1  ATCTGCCGTCGCGAAA-1  ATCTGCCGTGACTCAT-1  ATCTGCCTCGGTTCGG-1  ATGAGGGAGAGCCCAA-1  ATGAGGGAGTGGACGT-1  ATGAGGGGTACCGGCT-1  ATGAGGGGTCATCCCT-1  ATGAGGGTCACATACG-1  ATGCGATAGCAGGCTA-1  ATGCGATAGCCACGTC-1  ATGCGATAGCCGTCGT-1  ATGCGATCACCTGGTG-1  ATGCGATCATCGGAAG-1  ATGCGATGTAAATGAC-1  ATGCGATGTACAGACG-1  ATGCGATGTACTTGAC-1  ATGCGATGTATAAACG-1  ATGCGATTCAATCACG-1  ATGCGATTCATAGCAC-1  ATGCGATTCCGCGGTA-1  ATGCGATTCCGTCATC-1  ATGCGATTCGTTGACA-1  ATGCGATTCTCTTGAT-1  ATGGGAGAGAACAACT-1  ATGGGAGAGCCAGAAC-1  ATGGGAGAGGGCTCTC-1  ATGGGAGCAAGCCTAT-1  ATGGGAGCAAGTAGTA-1  ATGGGAGCATCGATGT-1  ATGGGAGCATGGTAGG-1  ATGGGAGGTCAGTGGA-1  ATGGGAGGTCCAGTTA-1  ATGGGAGGTGTGTGCC-1  ATGGGAGTCACAACGT-1  ATGTGTGAGCGTTTAC-1  ATGTGTGAGGATATAC-1  ATGTGTGAGGATGGAA-1  ATGTGTGCAATAACGA-1  ATGTGTGCATCAGTCA-1  ATGTGTGGTAAATGTG-1  ATGTGTGTCTGACCTC-1  ATTACTCAGAGTGACC-1  ATTACTCAGATGTGTA-1  ATTACTCAGGGTGTTG-1  ATTACTCCACCAGATT-1  ATTACTCCATGCAACT-1  ATTACTCCATTACCTT-1  ATTACTCGTCTGCCAG-1  ATTACTCTCACTATTC-1  ATTACTCTCCAAACTG-1  ATTATCCAGAGGGCTT-1  ATTATCCCAAGTAGTA-1  ATTATCCCAATCCGAT-1  ATTATCCGTCCTCCAT-1  ATTATCCGTCTCCATC-1  ATTATCCGTTGATTCG-1  ATTATCCTCCGCAAGC-1  ATTATCCTCGGTCCGA-1  ATTCTACAGAGGACGG-1  ATTCTACAGGATGGTC-1  ATTCTACCACACATGT-1  ATTCTACCACACCGCA-1  ATTCTACGTAGCGATG-1  ATTCTACTCCCTCAGT-1  ATTCTACTCGTGACAT-1  ATTGGACAGAGGTTGC-1  ATTGGACAGATGTAAC-1  ATTGGACAGGACTGGT-1  ATTGGACAGGCATGTG-1  ATTGGACGTCTGCAAT-1  ATTGGACGTGCCTGTG-1  ATTGGACGTTCGGGCT-1  ATTGGACTCACCCGAG-1  ATTGGACTCAGTACGT-1  ATTGGACTCATGCATG-1  ATTGGTGAGAGACTTA-1  ATTGGTGCAAAGGTGC-1  ATTGGTGGTCATCGGC-1  ATTGGTGTCGTACGGC-1  ATTGGTGTCTAACCGA-1  ATTTCTGAGCTGAACG-1  ATTTCTGCAACGATGG-1  ATTTCTGGTAGAGTGC-1  ATTTCTGTCGGCGCTA-1  CAACCAAAGACCACGA-1  CAACCAAAGCAGCGTA-1  CAACCAAAGTGAAGAG-1  CAACCAACAAATTGCC-1  CAACCAACAGTCCTTC-1  CAACCAACATGAACCT-1  CAACCAAGTACACCGC-1  CAACCAAGTAGAAGGA-1  CAACCAAGTAGGGTAC-1  CAACCAAGTTCCTCCA-1  CAACCAATCACCATAG-1  CAACCAATCCTTTCGG-1  CAACCAATCGGCTACG-1  CAACCTCAGAACAATC-1  CAACCTCAGCACACAG-1  CAACCTCAGCACAGGT-1  CAACCTCAGGATATAC-1  CAACCTCAGTAGGTGC-1  CAACCTCCAAGCCCAC-1  CAACCTCCAATACGCT-1  CAACCTCCATACCATG-1  CAACCTCCATCCAACA-1  CAACCTCCATGTAGTC-1  CAACCTCCATGTCCTC-1  CAACCTCGTACAAGTA-1  CAACCTCGTTTGGCGC-1  CAACCTCTCAAACGGG-1  CAACCTCTCATGTCTT-1  CAACTAGAGTGTACTC-1  CAACTAGAGTTGTCGT-1  CAACTAGGTAGCGCAA-1  CAACTAGGTCGTCTTC-1  CAACTAGTCCGTCAAA-1  CAAGAAAAGCGTAGTG-1  CAAGAAAAGTAAGTAC-1  CAAGAAACACCAGGCT-1  CAAGAAACATCCCATC-1  CAAGAAAGTATAATGG-1  CAAGAAAGTGCAGGTA-1  CAAGAAATCCGAGCCA-1  CAAGAAATCTAGAGTC-1  CAAGAAATCTTTACAC-1  CAAGATCAGAGCTATA-1  CAAGATCAGATGTGTA-1  CAAGATCAGTGACTCT-1  CAAGATCCAAACCCAT-1  CAAGATCCATAAAGGT-1  CAAGATCTCACAGGCC-1  CAAGATCTCTCCTATA-1  CAAGGCCAGAAGGTGA-1  CAAGGCCAGTACGTTC-1  CAAGGCCCATCTATGG-1  CAAGGCCGTACCGCTG-1  CAAGGCCGTAGAGTGC-1  CAAGGCCGTGCAGACA-1  CAAGTTGAGACAAGCC-1  CAAGTTGAGGATATAC-1  CAAGTTGCAAGCTGAG-1  CAAGTTGCAGACACTT-1  CAAGTTGGTGCGCTTG-1  CAAGTTGTCACCATAG-1  CAAGTTGTCTCGCATC-1  CACAAACAGCTCCTCT-1  CACAAACAGGCAGGTT-1  CACAAACCACCGAATT-1  CACAAACGTTGAGTTC-1  CACACAAAGAATGTTG-1  CACACAAAGAGTACCG-1  CACACAAAGCAGGTCA-1  CACACAAAGCTAGTCT-1  CACACAAAGGCTATCT-1  CACACAACAAAGAATC-1  CACACAACACCCATTC-1  CACACAACATAACCTG-1  CACACAAGTAGCACGA-1  CACACAAGTTACGGAG-1  CACACAATCAGTTAGC-1  CACACAATCTGAGGGA-1  CACACCTAGAGGTTAT-1  CACACCTAGCGCCTTG-1  CACACCTCAAGCTGAG-1  CACACCTCAGCCTGTG-1  CACACCTGTTACCGAT-1  CACACCTGTTGTCTTT-1  CACACCTTCGAGAACG-1  CACACTCAGATCGATA-1  CACACTCAGCCGATTT-1  CACACTCCATTTGCCC-1  CACACTCGTCCATGAT-1  CACACTCGTGTCAATC-1  CACACTCTCATCGGAT-1  CACACTCTCTACCAGA-1  CACACTCTCTCTAAGG-1  CACAGGCCACGACTCG-1  CACAGGCCAGGTCCAC-1  CACAGGCCATGCAATC-1  CACAGGCGTAAAGGAG-1  CACAGGCGTACCGTAT-1  CACAGGCGTGTCCTCT-1  CACAGTAAGGGTTCCC-1  CACAGTACAAGGACTG-1  CACAGTACAGAGCCAA-1  CACAGTACAGAGTGTG-1  CACAGTACAGGGATTG-1  CACAGTACATGGGAAC-1  CACAGTAGTAAACACA-1  CACAGTAGTAAGTGGC-1  CACAGTAGTCGAGATG-1  CACAGTAGTCTAGCCG-1  CACAGTAGTGCGAAAC-1  CACATAGAGTGTTTGC-1  CACATAGCAGCATGAG-1  CACATAGGTACCGGCT-1  CACATAGGTACGCACC-1  CACATAGTCAGAAATG-1  CACATAGTCAGGCCCA-1  CACATAGTCTTAACCT-1  CACATTTAGATCCGAG-1  CACATTTAGATGCCTT-1  CACATTTAGGCGTACA-1  CACATTTCAAACGTGG-1  CACATTTCAAGCTGTT-1  CACATTTCACGTCAGC-1  CACATTTGTTCGGGCT-1  CACCACTAGCCAGAAC-1  CACCACTAGGACGAAA-1  CACCACTAGTGTACTC-1  CACCACTCACGCCAGT-1  CACCACTGTAAACCTC-1  CACCACTGTATGAATG-1  CACCACTTCACCGTAA-1  CACCACTTCTAGCACA-1  CACCAGGAGGCTAGGT-1  CACCAGGAGTGGGCTA-1  CACCAGGCACTCGACG-1  CACCAGGGTCTCCCTA-1  CACCAGGGTGCCTGTG-1  CACCAGGTCATCGCTC-1  CACCAGGTCTGGCGTG-1  CACCAGGTCTGGTTCC-1  CACCTTGAGATGGCGT-1  CACCTTGAGCCTCGTG-1  CACCTTGAGGTTACCT-1  CACCTTGAGTGGCACA-1  CACCTTGCAGCTGTTA-1  CACCTTGCATTTCACT-1  CACCTTGTCAGATAAG-1  CACTCCAAGCTGGAAC-1  CACTCCAAGGAGCGTT-1  CACTCCAAGTCTTGCA-1  CACTCCACAATACGCT-1  CACTCCACACTGAAGG-1  CAGAATCAGGGCTTGA-1  CAGAATCCATGCAACT-1  CAGAGAGAGGGTGTTG-1  CAGAGAGCAACGATGG-1  CAGAGAGCAGTCGATT-1  CAGAGAGGTGGTTTCA-1  CAGAGAGGTTCAGTAC-1  CAGAGAGTCTGACCTC-1  CAGATCAAGGTAAACT-1  CAGATCACAAGAGGCT-1  CAGATCACAAGCGAGT-1  CAGATCACACATTTCT-1  CAGATCACACCGATAT-1  CAGATCACACGGACAA-1  CAGATCACAGGACCCT-1  CAGATCACAGTTCATG-1  CAGATCAGTCTGCAAT-1  CAGATCAGTGACCAAG-1  CAGATCAGTGTTCTTT-1  CAGATCAGTTCGTCTC-1  CAGATCATCAAACGGG-1  CAGATCATCTCACATT-1  CAGCAGCAGAGACTAT-1  CAGCAGCAGCCAGTTT-1  CAGCAGCAGCGTTTAC-1  CAGCAGCAGTACGATA-1  CAGCAGCCAAACGTGG-1  CAGCAGCCACGGTAAG-1  CAGCAGCCACTTCTGC-1  CAGCAGCCATCACAAC-1  CAGCAGCTCATAGCAC-1  CAGCAGCTCCGGGTGT-1  CAGCAGCTCCTAAGTG-1  CAGCAGCTCGAATCCA-1  CAGCAGCTCGCCTGTT-1  CAGCAGCTCTACTCAT-1  CAGCATAAGACAGACC-1  CAGCATAAGACAGAGA-1  CAGCATAAGATCTGAA-1  CAGCATAAGCGAAGGG-1  CAGCATAAGCGTCTAT-1  CAGCATAAGGCTAGCA-1  CAGCATAAGGCTAGGT-1  CAGCATACAAACAACA-1  CAGCATACAAGTCATC-1  CAGCATAGTACAGTGG-1  CAGCATATCCACGTGG-1  CAGCATATCGAACGGA-1  CAGCATATCGCAAACT-1  CAGCCGAAGGGTGTGT-1  CAGCCGAAGTGGAGTC-1  CAGCCGAAGTTAACGA-1  CAGCCGACAAGCTGTT-1  CAGCCGACAATGGTCT-1  CAGCCGACACATAACC-1  CAGCCGACATCACCCT-1  CAGCCGACATGCAATC-1  CAGCCGACATGGGAAC-1  CAGCCGACATGGTCAT-1  CAGCCGAGTCCGCTGA-1  CAGCCGATCAACGAAA-1  CAGCGACCAAGAGGCT-1  CAGCGACCAAGTACCT-1  CAGCGACCAGATGGGT-1  CAGCGACCAGTTAACC-1  CAGCTAAAGATCCTGT-1  CAGCTAAAGCTAAGAT-1  CAGCTAAAGGGAGTAA-1  CAGCTAACACTTAACG-1  CAGCTGGAGTAGGCCA-1  CAGCTGGAGTGCAAGC-1  CAGCTGGGTATATGGA-1  CAGCTGGGTTTGTTTC-1  CAGCTGGTCACGAAGG-1  CAGCTGGTCGTAGGTT-1  CAGGTGCAGCCCTAAT-1  CAGGTGCAGGCCCGTT-1  CAGGTGCAGTGCGATG-1  CAGGTGCCACACCGCA-1  CAGGTGCCACTTAAGC-1  CAGGTGCCAGCCTGTG-1  CAGGTGCCAGTATAAG-1  CAGGTGCGTCGAAAGC-1  CAGGTGCTCACTGGGC-1  CAGGTGCTCCTGCTTG-1  CAGTAACAGCCACCTG-1  CAGTAACAGGACAGAA-1  CAGTAACCAAGGTTTC-1  CAGTAACGTACCGTTA-1  CAGTAACGTACTTAGC-1  CAGTAACGTCTGGTCG-1  CAGTAACTCGCATGGC-1  CAGTAACTCGGTTAAC-1  CAGTCCTAGAATTGTG-1  CAGTCCTCAGTCGTGC-1  CAGTCCTCATTCCTGC-1  CAGTCCTGTAGCGTGA-1  CAGTCCTGTCTTGTCC-1  CAGTCCTGTTACGCGC-1  CAGTCCTGTTATCGGT-1  CAGTCCTGTTCCACTC-1  CAGTCCTGTTCTGTTT-1  CAGTCCTTCACGAAGG-1  CAGTCCTTCGCAAGCC-1  CAGTCCTTCGGTTAAC-1  CATATGGAGAGTACAT-1  CATATGGAGCGGCTTC-1  CATATGGAGTTAGCGG-1  CATATGGCAAGAAAGG-1  CATATGGCATTGGCGC-1  CATATGGGTAGAAAGG-1  CATATGGGTAGCTAAA-1  CATATGGGTCCAACTA-1  CATATGGTCAACGAAA-1  CATATGGTCACATGCA-1  CATATGGTCCAGAAGG-1  CATATGGTCTGTCCGT-1  CATATGGTCTGTCTCG-1  CATATTCAGATCTGAA-1  CATATTCAGGATGGAA-1  CATATTCAGGCATGTG-1  CATATTCAGTCGTTTG-1  CATATTCAGTGGGCTA-1  CATATTCAGTTGCAGG-1  CATATTCGTACGAAAT-1  CATATTCGTCACTTCC-1  CATATTCGTCTAAACC-1  CATATTCGTGCATCTA-1  CATATTCGTTCTCATT-1  CATATTCTCCAGAAGG-1  CATCAAGAGCATGGCA-1  CATCAAGAGTGTTGAA-1  CATCAAGCAAACTGTC-1  CATCAAGCAAAGGTGC-1  CATCAAGCAATAACGA-1  CATCAAGCACATCCGG-1  CATCAAGCACCAGTTA-1  CATCAAGCACGACGAA-1  CATCAAGGTTTGTTTC-1  CATCAAGTCCCAGGTG-1  CATCAAGTCGGTTAAC-1  CATCAAGTCTACCAGA-1  CATCAAGTCTCGTTTA-1  CATCAGAAGAGACTTA-1  CATCAGAAGTCTCCTC-1  CATCAGACAGTCAGAG-1  CATCAGACATGCAATC-1  CATCAGACATGCATGT-1  CATCAGAGTATGAATG-1  CATCAGATCACTTACT-1  CATCAGATCCGTAGGC-1  CATCAGATCGTAGGTT-1  CATCCACAGAGTGACC-1  CATCCACAGCAATCTC-1  CATCCACAGGACAGCT-1  CATCCACCAACTGCTA-1  CATCCACCACGACTCG-1  CATCCACCATCCCATC-1  CATCCACGTACAGTTC-1  CATCCACGTCAGATAA-1  CATCCACGTCCGTTAA-1  CATCCACGTCGGCTCA-1  CATCCACTCAACGGCC-1  CATCCACTCACGCATA-1  CATCCACTCTGACCTC-1  CATCGAACAACAACCT-1  CATCGAACAATCGAAA-1  CATCGAACAATGGTCT-1  CATCGAACACGGTAGA-1  CATCGAACAGACAAAT-1  CATCGAAGTCTCTCTG-1  CATCGAAGTGAAAGAG-1  CATCGAATCCACGCAG-1  CATCGGGAGCTAGTCT-1  CATCGGGAGTGACATA-1  CATCGGGCAAAGGAAG-1  CATCGGGGTAGGCTGA-1  CATCGGGGTTGTCGCG-1  CATCGGGTCAGAGACG-1  CATCGGGTCAGGATCT-1  CATCGGGTCGCATGAT-1  CATGACAAGAGAGCTC-1  CATGACAAGGCTAGGT-1  CATGACAAGTAGGCCA-1  CATGACAGTTATCCGA-1  CATGACATCCGCAGTG-1  CATGACATCGGCGCTA-1  CATGCCTAGCCCTAAT-1  CATGCCTAGTAGTGCG-1  CATGCCTAGTGAACAT-1  CATGCCTAGTTCGCAT-1  CATGCCTCAGCCTTTC-1  CATGCCTCAGCTCGAC-1  CATGCCTGTATATGGA-1  CATGCCTGTATTCTCT-1  CATGCCTGTCGGCATC-1  CATGCCTGTGACCAAG-1  CATGCCTTCACCGGGT-1  CATGCCTTCAGCATGT-1  CATGCCTTCCTAAGTG-1  CATGCCTTCTGCCAGG-1  CATGGCGAGGCACATG-1  CATGGCGAGTGCGTGA-1  CATGGCGAGTGTACTC-1  CATGGCGAGTTCGCGC-1  CATGGCGAGTTGTAGA-1  CATGGCGCAAGTCTAC-1  CATGGCGCACGTAAGG-1  CATGGCGTCAACACCA-1  CATGGCGTCACTTATC-1  CATTATCCACTGTCGG-1  CATTATCGTCACTGGC-1  CATTATCGTCCCTTGT-1  CATTATCTCCGTCATC-1  CATTATCTCTGGTTCC-1  CATTATCTCTTATCTG-1  CATTCGCAGTTTGCGT-1  CATTCGCCACTATCTT-1  CATTCGCGTAGAAAGG-1  CATTCGCGTCCGACGT-1  CATTCGCGTCTCTTAT-1  CATTCGCTCCCTTGCA-1  CATTCGCTCGTTTGCC-1  CCAATCCAGAACTCGG-1  CCAATCCAGACAGGCT-1  CCAATCCAGCTTCGCG-1  CCAATCCGTCTTTCAT-1  CCAATCCGTTTGGGCC-1  CCAATCCGTTTGTTTC-1  CCAATCCTCACTTCAT-1  CCACCTAAGAGACTAT-1  CCACCTAAGCTGTCTA-1  CCACCTAAGGCGACAT-1  CCACCTAAGTGTACTC-1  CCACCTAGTACAGCAG-1  CCACCTAGTACAGTGG-1  CCACCTAGTATATGGA-1  CCACCTAGTGTGTGCC-1  CCACCTAGTTAAGGGC-1  CCACCTATCAACACGT-1  CCACCTATCACATGCA-1  CCACCTATCACCACCT-1  CCACGGAAGAATTGTG-1  CCACGGAAGATAGTCA-1  CCACGGAAGGCAGTCA-1  CCACGGAAGTACGTTC-1  CCACGGAGTTAGAACA-1  CCACGGAGTTATGCGT-1  CCACGGATCGAGGTAG-1  CCACGGATCGGGAGTA-1  CCACGGATCGTCCGTT-1  CCACTACAGATATGCA-1  CCACTACAGCTGATAA-1  CCACTACAGTCATCCA-1  CCACTACCACAACTGT-1  CCACTACGTGCGATAG-1  CCACTACGTGTGGTTT-1  CCACTACTCCCTGACT-1  CCACTACTCTGGTGTA-1  CCAGCGACAATAGCAA-1  CCAGCGACATCGTCGG-1  CCAGCGAGTCGAGTTT-1  CCAGCGAGTGACTACT-1  CCAGCGAGTGGCAAAC-1  CCAGCGAGTTACGCGC-1  CCAGCGAGTTGAGTTC-1  CCAGCGATCAACACTG-1  CCAGCGATCCCTAACC-1  CCATGTCAGAGAACAG-1  CCATGTCAGAGCTTCT-1  CCATGTCAGTGAACGC-1  CCATGTCCAAAGCGGT-1  CCATGTCCACGAAAGC-1  CCATGTCCAGCTCCGA-1  CCATGTCCATTCACTT-1  CCATGTCGTAAGTGTA-1  CCATGTCGTCAAAGCG-1  CCATGTCGTGTCTGAT-1  CCATGTCGTTCCCGAG-1  CCATGTCGTTCCGGCA-1  CCATGTCTCTATGTGG-1  CCATGTCTCTCAAGTG-1  CCATGTCTCTCGAGTA-1  CCATGTCTCTGCAAGT-1  CCATTCGAGCTATGCT-1  CCATTCGAGGAGTTGC-1  CCATTCGGTGAAAGAG-1  CCATTCGGTTCTGTTT-1  CCATTCGTCCAAGTAC-1  CCATTCGTCCTACAGA-1  CCATTCGTCTCCCTGA-1  CCCAATCAGTTAAGTG-1  CCCAATCCAAACTGCT-1  CCCAATCCACAGACAG-1  CCCAATCCACCGTTGG-1  CCCAATCCATCACGAT-1  CCCAATCGTACGACCC-1  CCCAATCTCCAAACAC-1  CCCAATCTCCATGCTC-1  CCCAATCTCCTGCAGG-1  CCCAATCTCGCAGGCT-1  CCCAGTTAGAAACCAT-1  CCCAGTTAGGCCATAG-1  CCCAGTTCACTTGGAT-1  CCCAGTTCAGTCTTCC-1  CCCAGTTCATTCTTAC-1  CCCAGTTGTGCATCTA-1  CCCAGTTGTGGTGTAG-1  CCCAGTTGTTGCGCAC-1  CCCAGTTTCAACACTG-1  CCCATACCAAACTGCT-1  CCCATACCAAGACACG-1  CCCATACGTGAGCGAT-1  CCCATACGTGCCTGCA-1  CCCATACTCCGTAGGC-1  CCCATACTCGGTTCGG-1  CCCTCCTAGCTAACAA-1  CCCTCCTAGCTGGAAC-1  CCCTCCTAGGACACCA-1  CCCTCCTAGGAGTCTG-1  CCCTCCTAGGCTATCT-1  CCCTCCTAGGTAGCCA-1  CCCTCCTCAACTGGCC-1  CCCTCCTCAGCTCGAC-1  CCCTCCTCAGTAAGAT-1  CCCTCCTGTCTAGTCA-1  CCCTCCTTCCTGTACC-1  CCGGGATAGATCCCGC-1  CCGGGATAGCGTAGTG-1  CCGGGATAGGCATGTG-1  CCGGGATAGTCATGCT-1  CCGGGATCACGACGAA-1  CCGGGATCATATGGTC-1  CCGGGATGTACCGTTA-1  CCGGGATGTACTCGCG-1  CCGGGATTCAAGCCTA-1  CCGGTAGAGAAAGTGG-1  CCGGTAGAGTGTACCT-1  CCGGTAGCAGACGCAA-1  CCGGTAGCATGTAAGA-1  CCGGTAGGTCGATTGT-1  CCGGTAGTCGGATGGA-1  CCGGTAGTCTCCCTGA-1  CCGTACTAGTGAACGC-1  CCGTACTAGTGTACGG-1  CCGTACTGTAGAGCTG-1  CCGTACTTCAAGGTAA-1  CCGTACTTCATGTAGC-1  CCGTGGAAGCGATAGC-1  CCGTGGAAGTGTCTCA-1  CCGTGGACAAGCTGTT-1  CCGTGGAGTCAGCTAT-1  CCGTGGAGTTCCCGAG-1  CCGTTCAAGACTACAA-1  CCGTTCAAGATGTGTA-1  CCGTTCAAGCAACGGT-1  CCGTTCAAGCGCCTCA-1  CCGTTCAAGCTCCTCT-1  CCGTTCAAGTCGCCGT-1  CCGTTCAAGTGTCTCA-1  CCGTTCACAGGAATCG-1  CCGTTCACAGGTCGTC-1  CCGTTCACAGGTGCCT-1  CCGTTCACATGTTGAC-1  CCGTTCAGTACAAGTA-1  CCGTTCAGTATAAACG-1  CCGTTCATCCTCGCAT-1  CCGTTCATCGGAAATA-1  CCTAAAGAGACACGAC-1  CCTAAAGAGGCAGTCA-1  CCTAAAGAGTCCGTAT-1  CCTAAAGAGTGGAGAA-1  CCTAAAGCAAGACACG-1  CCTAAAGCAGTTTACG-1  CCTAAAGGTCTGGTCG-1  CCTAAAGGTGCTGTAT-1  CCTAAAGGTTCCATGA-1  CCTAAAGTCCTTGGTC-1  CCTAAAGTCTAGAGTC-1  CCTAAAGTCTGGCGTG-1  CCTAAAGTCTTTCCTC-1  CCTACACAGAACAACT-1  CCTACACAGATCGATA-1  CCTACACAGGAGTCTG-1  CCTACACCAATAGCGG-1  CCTACACCATCACAAC-1  CCTACACCATGCCTAA-1  CCTACACGTCACACGC-1  CCTACACGTCTCTCTG-1  CCTACACGTTCAGACT-1  CCTACACGTTTGTTGG-1  CCTACACTCAAAGTAG-1  CCTACACTCATAACCG-1  CCTACACTCTAGAGTC-1  CCTACCAAGGGAGTAA-1  CCTACCAAGTCGCCGT-1  CCTACCACAAAGTGCG-1  CCTACCACACCTGGTG-1  CCTACCACAGGTCTCG-1  CCTACCAGTACCAGTT-1  CCTACCAGTCGCATAT-1  CCTAGCTAGACGACGT-1  CCTAGCTCAGCTGGCT-1  CCTAGCTCATGCATGT-1  CCTAGCTCATTTCAGG-1  CCTAGCTGTAAGTAGT-1  CCTAGCTTCCGTCATC-1  CCTATTAAGGCGTACA-1  CCTATTAAGTCTCGGC-1  CCTATTACAACACGCC-1  CCTATTACACGCGAAA-1  CCTATTACAGTGGAGT-1  CCTATTACATAGGATA-1  CCTATTAGTAAACACA-1  CCTATTATCCGCAAGC-1  CCTATTATCCGCGGTA-1  CCTCAGTAGCAACGGT-1  CCTCAGTAGCACGCCT-1  CCTCAGTAGCCACGTC-1  CCTCAGTAGGAGTACC-1  CCTCAGTGTGAGGGTT-1  CCTCAGTTCTTGGGTA-1  CCTCTGAAGCGTTTAC-1  CCTCTGAAGTTTAGGA-1  CCTCTGAGTCATGCAT-1  CCTCTGAGTTTGACAC-1  CCTCTGAGTTTGGCGC-1  CCTCTGATCACCAGGC-1  CCTTACGAGTGGTCCC-1  CCTTACGCACGGACAA-1  CCTTACGCAGAGTGTG-1  CCTTACGCAGCTATTG-1  CCTTACGCATCGGGTC-1  CCTTACGCATGCAATC-1  CCTTACGTCTCGTATT-1  CCTTACGTCTGCAAGT-1  CCTTCCCAGCGATCCC-1  CCTTCCCAGCTAGTTC-1  CCTTCCCCACCGAATT-1  CCTTCCCGTACGAAAT-1  CCTTCCCGTCGACTAT-1  CCTTCCCGTTATGCGT-1  CCTTCCCGTTCCACTC-1  CCTTCCCTCAGAAATG-1  CCTTCCCTCGTGGACC-1  CCTTCGAAGCGTGAGT-1  CCTTCGAAGTCGATAA-1  CCTTCGACACATTAGC-1  CCTTCGACACTAGTAC-1  CCTTCGACATCCCATC-1  CCTTCGATCACCGTAA-1  CCTTCGATCGTCCAGG-1  CCTTTCTAGAAAGTGG-1  CCTTTCTAGAGCAATT-1  CCTTTCTAGCAAATCA-1  CCTTTCTAGCGTGTCC-1  CCTTTCTAGGAGCGAG-1  CCTTTCTAGGATGTAT-1  CCTTTCTCAGCTTAAC-1  CCTTTCTGTTAAGAAC-1  CCTTTCTTCACCTTAT-1  CCTTTCTTCGAGAGCA-1  CCTTTCTTCTGAGGGA-1  CGAACATAGACTGTAA-1  CGAACATAGAGGTTAT-1  CGAACATAGTAGGTGC-1  CGAACATCAAACCCAT-1  CGAACATCACAGGCCT-1  CGAACATCAGCTGGCT-1  CGAACATGTCCTAGCG-1  CGAACATGTGTGACGA-1  CGAACATTCGGAATCT-1  CGAATGTAGACAGAGA-1  CGAATGTAGCCACGCT-1  CGAATGTAGCCCAGCT-1  CGAATGTAGGATTCGG-1  CGAATGTAGTATTGGA-1  CGAATGTGTACTCAAC-1  CGAATGTGTGCAGACA-1  CGAATGTGTTGGTTTG-1  CGAATGTTCATGCTCC-1  CGAATGTTCTCAAACG-1  CGACCTTAGACAATAC-1  CGACCTTAGAGAACAG-1  CGACCTTAGGCATGTG-1  CGACCTTAGTTAGCGG-1  CGACCTTCAACACCTA-1  CGACCTTCACATCTTT-1  CGACCTTCAGCTGTAT-1  CGACCTTCATACAGCT-1  CGACCTTTCTTCATGT-1  CGACTTCAGCGTCTAT-1  CGACTTCAGTACGCGA-1  CGACTTCCAAACAACA-1  CGACTTCCATTACCTT-1  CGACTTCGTCGGCTCA-1  CGACTTCTCACCAGGC-1  CGACTTCTCAGCTCTC-1  CGACTTCTCGCAGGCT-1  CGACTTCTCTCCCTGA-1  CGAGAAGGTCGCGGTT-1  CGAGAAGGTGAAATCA-1  CGAGAAGGTTTAAGCC-1  CGAGAAGTCGGGAGTA-1  CGAGCACAGAGTACCG-1  CGAGCACAGCACGCCT-1  CGAGCACAGCGCCTCA-1  CGAGCACAGGGATACC-1  CGAGCACAGTTCGCGC-1  CGAGCACCACGTCTCT-1  CGAGCACCATCCTTGC-1  CGAGCACGTTAAAGAC-1  CGAGCACTCAGCGACC-1  CGAGCACTCGCTTAGA-1  CGAGCCAAGAAGAAGC-1  CGAGCCAAGCGGATCA-1  CGAGCCAAGGTGATTA-1  CGAGCCAAGTGGCACA-1  CGAGCCACAAACAACA-1  CGAGCCACAATGGTCT-1  CGAGCCACACCCATTC-1  CGAGCCACAGCCAATT-1  CGAGCCACAGTTCATG-1  CGAGCCACATGGAATA-1  CGAGCCAGTTAAAGTG-1  CGAGCCATCGCTTGTC-1  CGAGCCATCTGCGTAA-1  CGATCGGAGAGCTTCT-1  CGATCGGAGCGATATA-1  CGATCGGAGGAATTAC-1  CGATCGGAGTACTTGC-1  CGATCGGAGTCAATAG-1  CGATCGGAGTCCGTAT-1  CGATCGGAGTGGTCCC-1  CGATCGGCACATGACT-1  CGATCGGCAGATCTGT-1  CGATCGGCATTTCACT-1  CGATCGGGTATATCCG-1  CGATCGGGTTCGCGAC-1  CGATCGGTCCACTCCA-1  CGATCGGTCCGCATAA-1  CGATGGCAGACACGAC-1  CGATGGCAGCACCGCT-1  CGATGGCAGTACACCT-1  CGATGGCCAAAGGCGT-1  CGATGGCGTCTCTCTG-1  CGATGGCGTGGGTCAA-1  CGATGGCGTTTGCATG-1  CGATGGCTCGGAGCAA-1  CGATGGCTCTGCAAGT-1  CGATGTAAGAGGTAGA-1  CGATGTAAGTACGCGA-1  CGATGTACACGTTGGC-1  CGATGTACATAGAAAC-1  CGATGTACATTGGTAC-1  CGATGTAGTAGCGCAA-1  CGATGTAGTATAGGTA-1  CGATGTAGTTTACTCT-1  CGATGTATCAGATAAG-1  CGATGTATCCAAAGTC-1  CGATGTATCCGCATCT-1  CGATTGAAGCGTTTAC-1  CGATTGAAGTCGCCGT-1  CGATTGAAGTGAATTG-1  CGATTGACAAGCGAGT-1  CGATTGACACTTCTGC-1  CGATTGACAGATGGCA-1  CGATTGACAGCCTTTC-1  CGATTGACATCGATGT-1  CGATTGAGTACCCAAT-1  CGATTGAGTCTAGCGC-1  CGATTGATCAAGCCTA-1  CGATTGATCCATTCTA-1  CGATTGATCCGTTGTC-1  CGATTGATCTGGTGTA-1  CGCCAAGAGTATTGGA-1  CGCCAAGGTTACGGAG-1  CGCCAAGTCCGCGGTA-1  CGCGGTACAATCTGCA-1  CGCGGTACACATCCAA-1  CGCGGTACACTAAGTC-1  CGCGGTAGTATAGTAG-1  CGCGGTAGTCGCTTCT-1  CGCGGTAGTTAAGAAC-1  CGCGGTAGTTTGGGCC-1  CGCGGTATCAACACCA-1  CGCGGTATCGCAAGCC-1  CGCGTTTAGTGAATTG-1  CGCGTTTCACAGGCCT-1  CGCGTTTCATATACGC-1  CGCGTTTCATGGGACA-1  CGCGTTTGTCCAACTA-1  CGCGTTTGTGCAACGA-1  CGCGTTTGTTAAGGGC-1  CGCGTTTTCTCGCATC-1  CGCTATCAGGATCGCA-1  CGCTATCCATT
CGE10x_counts.csv
CGE10x

data_processing:
gene expression counts matrix in csv format containing analyed CGE E14.5 WT progenitors and early postmitotic interneurons - samples in columns annotated by their barcodes, genes in rows with gene symbol notation
Cell Ranger software was used for mapping reads to the mm10 Mus Musculus genome.
Quality Control beyond Cell Ranger output: we discarded cells epressing less than 1000 genes or more than 15% mitochondrial reads. Non-interneuron populations were excluded by clustering.
mm10 v3.0.0.

source_name: embryonic brain CGE

extract_protocol:
E14.5 C57BL/6 WT brains were extracted in ice-cold HBSS and sectioned. Caudal Ganglionic Eminence microdissected tissue was then incubated in 0.05% Trypsin at 37°C for 5 minutes. After digestion, FBS was added and cells were mechanically dissociated via pipetting and centrifuged 5 minutes at 300g. Cell pellet was then suspended in 1ml HBSS and filtered using a 70um strainer.
Cell suspension was loaded into a 10X Chromium controller and processed with the Single Cell 3' v2 reagent kit. Single cel libraries were then sequenced using a HiSeq 4000 instrument.

value: embryonic brain CGE


title: ZT4_18C_WT_Rep1

status: Public on Jun 30 2023

type: SRA

city: Evanston

first: Ravi

last: Allada

state: Illinois

address: 2200 Campus Drive Room 2-201

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
FASTQ files were quantified with kallisto v0.46.2 (single read mode, bootstrap samples n=25)
Obtained transcripts were aggregated to gene level counts with the tximport R library.
Data was quantified as transcripts per million (TPM).
Genome_build: dmel_r6.43
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with TPM counts for every gene and every sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: Fat Body

growth_protocol: All the flies used for experiments were first raised on a standard yeast-cornmeal-molasses based diet under a light-dark (LD) 12:12h cycle. Young mated female (~3 days old) flies (w^{1118}: Bloomington stock number 5905, Clk-Jrk: backcrossed 7 times to w^{1118}) of ~24 hours cohorts were entrained at either 25oC or 18oC for 5 days in 12L:12D cycles on a standard SY (sucrose: 150 g/L, yeast: 150 g/L) diet.

extract_protocol:
To collect dissected fat body samples at 2-hour and 4-hour intervals from ZT0 (set to 8AM) to ZT22 set (set to 10PM) during the daytime only, flies were entrained in two separate incubators with inverse light:dark schedule (LD and DL). On the day of sampling, flies were directly dissected without dry ice to harvest fat tissues in the abdomen. Pinned flies were cut to remove organs in the abdomen (intestine, ovaries, malpighian tubules, etc). Fat tissues attached to epidermis was collected. Dissected fat body tissues from 10 flies were homogenized in pH 7.4 PBS for 2 min using a Kontes motor and pestle, and were incubated TRIzol LS Reagent (Thermo Fisher, Waltham, MA) for 15 min. RNA was extracted according to the manufacturer’s instructions and residual DNA in the homogenized samples was removed by RNAse free DNase I (Thermo Fisher Scientific). Quality of RNA samples were checked with Agilent 2100 Bioanalyzer.
cDNA library was constructed with poly(A) selected mRNA using Truseq RNA library preparation kit and then sequenced at the Genomics Core Facility at the University of Chicago on Illumina HiSeq 2000 System.

tag: tissue

value: Fat Body

tag: strain

tag: treatment

tag: time


title: C9_2

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

data_processing:
clean data were mapped to mouse genome mm10 by hisat2
reads count per gene is caculated by featurecount
Assembly: mm10
Supplementary files format and content: gene annotation with reads count

organism: Mus musculus

source_name: Cortex

extract_protocol:
Surgically resected cortical tissue was homogenized using a glass dounce homogenizer in 2 ml of ice-cold Nuclei EZ lysis buffer (#EZ PREP NUC-101, Sigma) and was incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C, washed with 4 ml ice-cold Nuclei EZ lysis buffer and, incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were resuspended in 1 ml of nuclei suspension buffer (NSB) consisting of 1XPBS, 1%BSA (#AM2618, Thermo Fisher Scientific) and 0.2U/ul RNAse inhibitor (#AM2694, Thermo Fisher Scientific) and were filtered through a 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art). Nuclei concentration was determined using 0.4% Trypan Blue (#15250061, Thermo Fisher Scientific). Final concentration of 1000 nuclei/μl was adjusted with NSB.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 according to the manufacturer’s protocol.

value: Cortex

tag: genotype

value: C9orf72+/-;C9-BAC with AAV-C9orf72


title: C9_1


title: P2_E01_530_mono_40

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

country: United Kingdom

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

data_processing:
Smart-Seq2
Genome_build: mm10
Supplementary_files_format_and_content: counts

molecule: polyA RNA

source_name: peripheral blood

growth_protocol: Cells were isolated from B6Tg(MMTV-PyMT)634Mul/Lellj mice bearing late stage tumors (upto 24mm diameter) or from aged matched  C57BL/6JCrl controls

extract_protocol:
Cells were sorted into 96 well place containing 2 ul of lysis buffer in each well
as per Smart-seq2 protocol (Picelli et al 2013)
Nextera; 75bp + 75bp; HiSeq2500

treatment_protocol: 40µL of blood containing x µl 0.5M EDTA was lysed 400µL RBC lysis buffer (Biolegend), cells washed in excess 10% FCS/PBS, and lysis repeated. Cells were then blocked with 20 µL block and stained with antibodies in 30µL FACS buffer and individual live, single CD11b+ CD45+ CD115+ CD3- CD19-NK1.1- cells were FACS sorted into 96 well plates containing 2 ul of the lysis buffer (0.2% Triton X100 containing 1:20 RNASE inhibitor) per well.

tag: cell type

value: monocytes

value: TUM

value: peripheral blood


title: P2_E01_530_mono_39


title: P2_E01_530_mono_38


title: P2_E01_530_mono_37


title: Liver_Control_T01_rep1

city: Guangzhou

first: Xiaowen

last: Zhou

state: Guangdong

address: No.232, East Waihuan Road, Guangzhou Higher Education Mega Centre, Panyu District

country: China

institute: Guangzhou University of Chinese Medicine

data_processing:
Low quality reads, such as only adaptor, unknown nucleotides>5%, or Q20 <20% (percentage of sequences with sequencing error rates <1%), were removed by perl script.
The clean reads that were filtered from the raw reads were mapped to honeybee (Apis mellifera) genome (OGSv3.2) using Tophat2 (Kim, Pertea et al. 2013) software.
The aligned records from the aligners in BAM/SAM format were further examined to remove potential duplicate molecules.
Gene expression levels were estimated using FPKM values (fragments per kilobase of exon per million fragments mapped) by the Cufflinks software (Trapnell, Williams et al. 2010).
Assembly: Rnor_6.0_release85
Supplementary files format and content: tab-delimited text file include RPKM values for 16 Samples

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Before treatment, the rat model of HLP was established by the fed with high-fat diet for 4 weeks.

extract_protocol:
Total RNA was extracted from liver tissue samples  by using TRIzol reagent.
The cDNA library was constructed following the manufacturer’s instructions of NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, E7530）and NEB Next Multiplex Oligos for Illumina ( NEB, E7500). In briefly, the enriched mRNA was fragmented into approximately 200nt RNA inserts, which were used to synthesize the first-strand cDNA and the second cDNA. The double-stranded cDNA were performed end-repair/dA-tail and adaptor ligation. The suitable fragments were isolated by Agencourt AMPure XP beads (Beckman Coulter, Inc.), and enriched by PCR amplification. Finally, the constructed cDNA libraries of the honey bee were sequenced on a flow cell using an Illumina HiSeq™ sequencing platform.

treatment_protocol: In the treatment phase, the rats in control group (0.9% saline) were fed with normal diet and the rat model were continuously supplied with HFD but regrouped into three groups according to different administration solution: model group (0.9% saline), 12.6g/kg HTJZD group and 4.54g/kg PC-AR group for 4 weeks. Each rat was given an intragastric dose of 1 mL/100g.

value: Liver

tag: group

value: Control

value: saline


title: PBS2


title: PBS3


title: PBS1


title: P2_E01_530_mono_36


title: P2_E01_530_mono_35


title: wt2

value: Wild Type


title: P2_E01_530_mono_34


title: wt1


title: Spleen Sham 2

type: RNA

city: Gainesville

first: Robert

last: Maile

state: FL

address: 1600 SW Archer Road

department: Surgery

institute: University of Florida

hyb_protocol: Standard nanostring mRNA hybridisation protocols.

data_processing: nsolver v3

source_name: mRNA from spleen

extract_protocol: Cell suspensions were prepared from the spleens of mice red blood cells were lysed with ACK Lysis Buffer (0.15M NH4Cl4, 1mM KHCO3, and 0.1 Mm Na2 EDTA in water) before lysing with RLT lysis buffer and processed using the RNeasy kit. Total RNA was quantified using a nanodrop 2000 spectrophotometer.

treatment_protocol: Mice were treated with 1x1010 MSC-EVs inravenously 72 hours after exposure to 9 Gys of WBIR or RCI. 48 hours later the spleens were isolated from these mice and processed for RNA.

tag: injury, treatment


title: RCI 2

label_protocol: Standard nanostring mRNA hybridisation protocols.

value: RCI, PBS


title: Spleen Sham 3


title: WBIR w/ MSC-EVs 1

value: WBIR, MSC-EVs


title: WBIR 3

value: WBIR


title: RCI 1


title: WBIR w/ MSC-EVs 2


title: WBIR w/ MSC-EVs 3


title: RCI 3


title: WBIR 1


title: WBIR 2


title: P2_E01_530_mono_33


title: RCI w/ MSC-EVs 3

value: RCI, MSC-EVs


title: snRNA-seq WT

data_processing:
Single-nuclei RNA-seq data was processed using mkfastq command from 10X Genomics CellRanger v3.0.1.
Assembly: mm10

value: WT


title: P2_E01_530_mono_32


title: snRNA-seq HOM


title: RCI w/ MSC-EVs 1


title: Sham 3

hyb_protocol: Standard nanostring mRNA hybdrization protocols.

scan_protocol: Long

source_name: mRNA from macrophages

extract_protocol: RNA was isolated using Qiagen RNAeasy isolation kit.

treatment_protocol: RAW Macrophages were exposed to 3.0x107 EVs isolated from mice 3 days or 7 days after exposure to either 2 or 9 grays of WBIR for 24 hours in the presence of LPS. After exposure, cells were lysed with Trizol.

tag: dose, days after dose


title: RCI w/ MSC-EVs 2


title: Spleen Sham 1


title: 01-21-2N

type: genomic

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 11.0 using default settings.

data_processing: Data was extracted from the TIFF files using Agilent FE 11.  The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2)[23]. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval, and to the square root of the number of probes in the interval.

molecule: genomic DNA

organism: Homo sapiens

source_name: Pancreatic ductal adenocarcinoma

label_protocol: DNAs from frozen tissue were treated with DNAse 1 prior to Klenow-based labeling. High molecular weight templates were digested for 30 minutes. In each case 1 ul of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols [22]. All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to CGH arrays (Agilent Technologies, Santa Clara, CA).

growth_protocol: Fresh tumor samples of liver metastasis from pancreas ductal adenocarcinoma cancer patients were flash-frozen and maintaned at -80 degrees C.

extract_protocol: Biopsies were minced in the presence of NST buffer and DAPI according to published protocols (Holley et al, 2012). Nuclei were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Aria III cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm. DNA content and cell cycle were analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA).DNAs were extracted using Qiagen micro kits (Qiagen Valencia, CA).

tag: tissue source

value: Patient biopsy

tag: tissue type

value: frozen tissue

tag: flow sort content

value: Human tumor liver metastasis

source_name: Reference pooled 46XX

tag: reference

value: Normal female genome


title: Sham 2

label_protocol: Standard nanostring mRNA hybdrization protocols.


title: P2_E01_530_mono_31


title: R27 3


title: R27 2


title: 01-21-AN


title: Sham 1


title: R27 1


title: snRNA-seq HET

value: Cortex


title: P2_E01_530_mono_30

value: monocytes


title: snRNA-seq BAC


title: P2_E01_530_mono_27

value: TUM


title: D7_Bcl6KO_IEL [scRNA-seq]

city: La Jolla

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Dr

institute: UCSD

data_processing:
data were processed by cellranger 2.1.0 with default parameter, using mm10 as reference.
Raw cell-reads were then loaded to R using the cellrangerRkit package. The scRNA-seq dataset was then further filtered based on gene numbers and mitochondria gene counts tototal counts ratio. Only cells with > 400 genes,UMI > 0,and 0.5% ~ 20% of their UMIs mappingto mitochondria genes were kept for downstream analysis.
For the scRNA-seq, the first 16 bp of R1 is the cell barcode and the next 10bp (17-26bp) is the UMI.
mm10
Genome_build: CellRanger output of filtered gene matrix with barcodes & features files
Supplementary_files_format_and_content: tsv, mtx

source_name: D7 SI IEL Bcl6KO SMARTA

extract_protocol:
Single cell libraries were prepared according to the protocol for 10X Genomics for 3' Gene Expression. Approximately 10,000 sorted CD4+ cells were loaded and partitioned into Gel Bead In-Emulsions (GEM). scRNA libraries were sequenced on a HiSeq4000 (Illumina).
3' Transcriptome sequencing (10X genomics V3)

tag: age

value: 6-16 Weeks

value: Small Intestine Epithelium

tag: time point

tag: agent

value: LCMV-Armstrong


title: D7_Bcl6KO_LPL [scRNA-seq]

source_name: D7 SI LPL Bcl6KO SMARTA

value: Small Intestine Lamina Propria


title: R23 1


title: R97 2


title: P2_E01_530_mono_28

value: peripheral blood


title: R97 1


title: D7_Bcl6KO_SPL [scRNA-seq]

source_name: D7 Spleen Bcl6KO SMARTA

value: Spleen


title: R23 2


title: R97 3


title: R23 3


title: D7_LPL_2 [scRNA-seq]

source_name: D7 SI LPL SMARTA


title: P2_E01_530_mono_24


title: P2_E01_530_mono_29


title: P2_E01_530_mono_25


title: R93 3


title: R93 2


title: D7_SPL_2 [scRNA-seq]

source_name: D7 Spleen SMARTA


title: CD56 ILC, in vitro, week 4, scRNAseq

city: LUND

first: Dang

middle: Nghiem

last: Vo

address: B12 Biomedical Center, Klinikgatan 26

department: Department of Laboratory Medicine

country: Sweden

institute: Lund University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
obtained sequence reads were processed using CellRanger (10X Genomics) pipeline
Assembly: hg38
Supplementary files format and content: tab-separated values files and count matrix file

source_name: cord blood derived cells from in vitro culture

growth_protocol: CD34 hematopoietic progenitors from cord blood are cultured on OP9 stroma, in presence of IL-3, IL-7, IL-15, SCF and FL cytokines in OptiMEM medium.

extract_protocol:
Differentiated cells after 4 week in vitro culture are harvested and subjected to NK cell enrichment column (negative selection). Purified CD56-positive cells are directly proceeded to single-cell droplet generation with 10X Genomics platform and further undergone library preparation.
library preparation was done according to the Chromium Single Cell 3’ Reagent Kit v3.1 protocol

value: primary cultured cells


title: P2_E01_530_mono_26


title: AGS cells, BYL719 Treated, CBFB KO Cl.2 Rep 2

city: Durham

first: Micah

last: Luftig

state: North Carolina

address: 213 Research Dr, 0045 CARL

institute: Duke University

data_processing:
Read assembly, trimming and QC (performed by third party)
HISAT2
DESeq2
Assembly: hg38
Supplementary files format and content: aligned reads as bam file for each sample
Supplementary files format and content: DESeq analysis files

source_name: AGS

growth_protocol: AGS cells were maintained in DMEM/F-12K nutrient medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen)
RNA library was prepared by Novogene (Beijing, China) following their protocol

treatment_protocol: Cells were treated for 24 hours with 1 uM BYL719 (Selleckchem)

tag: cell line

value: AGS

value: gastric adenocarcinoma

value: CBFB knockout

value: 1 uM BYL719, 24 hours


title: AGS cells, BYL719 Treated, CBFB KO Cl.2 Rep 1


title: AGS cells, BYL719 Treated, CBFB KO Cl.1 Rep 2


title: AGS cells, untreated, CBFB KO Cl.2 Rep 1


title: P2_E01_530_mono_23

tag: tissue


title: AGS cells, BYL719 Treated, CBFB KO Cl.1 Rep 1


title: D7_LPL_1 [scRNA-seq]

tag: strain


title: AGS cells, untreated, CBFB KO Cl.1 Rep 1

tag: treatment


title: D7_IEL_2 [scRNA-seq]

source_name: D7 SI IEL SMARTA


title: AGS cells, untreated, CBFB KO Cl.1 Rep 2


title: P2_E01_530_mono_22


title: AGS cells, untreated, CBFB KO Cl.2 Rep 2


title: AGS cells, BYL719 Treated, BYL719-Resistant Cl.3

value: WT


title: AGS cells, BYL719 Treated, BYL719-Resistant Cl.2


title: P2_E01_530_mono_21


title: AGS cells, BYL719 Treated, BYL719-Resistant Cl.1


title: D7_SPL_1 [scRNA-seq]


title: R93 1


title: AGS cells, untreated, BYL719-Resistant Cl.1


title: D21_LPL_2 [scRNA-seq]

source_name: D21 SI LPL SMARTA


title: AGS Cells, BYL719 Treated, Biol Rep 3


title: P2_E01_530_mono_20


title: AGS cells, untreated, BYL719-Resistant Cl.3


title: AGS Cells, BYL719 Treated, Biol Rep 2


title: AGS cells, untreated, BYL719-Resistant Cl.2


title: D21_SPL_2 [scRNA-seq]

source_name: D21 Spleen SMARTA


title: P2_E01_530_mono_17


title: AGS Cells, BYL719 Treated, Biol Rep 1


title: P2_E01_530_mono_18


title: P2_E01_530_mono_19


title: D21_SPL_1 [scRNA-seq]


title: AGS cells, untreated, Biol Rep 2


title: D21_LPL_1 [scRNA-seq]


title: P2_E01_530_mono_16


title: AGS cells, untreated, Biol Rep 1


title: P2_E01_530_mono_14


title: P2_E01_530_mono_13


title: AGS cells, untreated, Biol Rep 3


title: Zebrafish_KO3

city: Chongqing

first: Hongxiang

last: Xu

address: Tiansheng Road

institute: Southwest University

data_processing:
Base Calling:CASAVA
Data filtering: Cutadapt
Read alignment:Hisat2
Abundance measurement:Subread
DEG analysis: DESeq2
Assembly: Danio rerio refrence genome
Supplementary files format and content: raw counts

organism: Danio rerio

source_name: liver

extract_protocol:
Culture WT, ΔMMAR_0267 and ΔMMAR_0267:: MMAR_0267 M. marinum on 7H10 plates, pick a single colony and culture it in liquid medium. Shake the culture at 30°C until the OD600 value reaches approximately 0.5. Select healthy adult zebrafish from a population and acclimate them in fresh water for 24 hours before grouping. Centrifuge the M. marinum culture, remove the supernatant, wash the bacteria with PBS three times, and finally dilute the bacterial suspension to 10^8 CFU/mL. Place the zebrafish into a new dish, inject 10μL of bacterial suspension into the zebrafish abdomen. After infection, return the zebrafish to the acclimation water. At different time points after infection, observe the fish for signs of illness and death. Simultaneously, isolate and identify the pathogenic bacteria from dead fish to determine the species and quantity of the infecting pathogen.
After the samples pass the test, use magnetic beads with Oligo (dT) to enrich Eukaryote mRNA. Subsequently, a fragmentation buffer was added to randomly interrupt the mRNA. Using mRNA as a template, the first strand of cDNA was synthesized using six base random primers. Then, buffer, dNTPs, and DNA polymerase I were added to synthesize the second strand of cDNA. The double stranded cDNA was purified using AMPure XP beads. The purified double stranded cDNA was subjected to end repair, A-tail addition, and sequencing connections. Then, AMPure XP beads were used for fragment size selection, and PCR enrichment was performed to obtain the final cDNA library.

value: liver

value: KO


title: Zebrafish_KO2


title: Zebrafish_MM2

value: MM


title: GBM8401 cells (bio rep2)

city: Kaohsiung

first: Jui-Pei

last: Weng

address: No.70 Lien-hai Road

country: Taiwan

institute: National Sun Yat-sen University

data_processing:
Illumina official tool, BCL2FASTQ conversion Software v2.20 was used to convert BCL files from the Illumina sequencing platform.
TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases.
Trimmed reads were aligned to the reference genome sequence using HISAT2 v2.1.0 aligner to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
Differential expression analysis was performed using CUFFDIFF of CUFFLINKS package v2.2.1 to produce gene/transcript read count and FPKM profiles for each group of samples, then functional enrichment assay was performed using clusterProfiler v3.6.
Assembly: GRCh38.p10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: brain

growth_protocol: The human brain malignant glioma cell line, GBM8401, was mantained in RPMI1640 with 10% supplemented with 10% fetal bovine serum (Gibco), 50 U/mL peni-cillin, and 50 mg/mL streptomycin (Sigma) . Cell lines were cultured in a humidified atmosphere of 5% CO2 mixed with 95% air at 37°C

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen, USA) according to the instruction manual. Purified RNA was quantified at OD260nm using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 LabChip kit (Agilent Technology, USA).
Agilent's SureSelect Strand-Specific RNA Library Preparation Kit was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection

treatment_protocol: TMZ-resistant cells were induced in GBM8401 cell lines. The TMZ-resistant cells were generated from 200 μM TMZ (Sigma)-containing medium, and the fresh medium was changed every 2-3 days for 140 days (21).

value: brain

value: Human brain glioblastoma multiforme

value: parental


title: GBM8401 TMZ-resistant cells (bio rep2)

value: GBM8401 TMZ-resistant cells

value: TMZ-resistant


title: GBM8401 TMZ-resistant cells (bio rep1)


title: P2_E01_530_mono_15

source_name: peripheral blood

value: monocytes

value: TUM


title: P2_E01_530_mono_12

value: peripheral blood


title: Zebrafish_MM1


title: Zebrafish_MM3


title: P2_E01_530_mono_11


title: human CD34+ cells, CITE-seq GEX

city: Bethesda

first: Daisuke

last: Araki

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

description:
10x Genomics
GEX

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
Illumina sequencer’s base call files (BCLs) were demultiplexed, for each flow cell directory, into FASTQ files using Cellranger mkfastq with default parameters (v 6.1.2) in NIH Helix/Biowulf High Performance Computation (HPC) system.
FASTQ files were then processed using Cellranger Antibody Capture count with default parameters in NIH Helix/Biowulf HPC system.
Internally, the software relies on STAR for aligning reads to a pre-build filtered human reference genome relying on GRCh38, while genes are quantified using ENSEMBL genes as gene model.
The output of Cellranger is a filtered gene-barcode matrix containing the UMI counts for each gene.
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: CD34+ cells

extract_protocol:
Human CD34+ cells edited with Cas9 alone (Cas9 group), Cas9+AAVS1-targeting gRNA (RNP group), or Cas9+AAVS1-targeting gRNA+GSE56 (RNP/GSE56 group) were transplanted into busulfan-conditioned NSG mice, and these mice subsequently received 3 days of PBS or G-CSF. Then, each mouse was euthanized and harvested for bone marrow cells and human CD34+cells were isolated using immunomagnetic beads. These CD34+ cells from a total of 6 mice were individually stained with Total seq B CITE-seq antibodies (CD38, CD45RA, CD90, CD49f) + hashtag oligo antibodies 1-6. Then, FACS sort was used to purify ~2,500 cells from each group, and subsequently pooled for CITE-seq library preparation.
3’ v3.1 GEX libraries were constructed according to 10x Genomics protocol. 3’ v3.1 GEX and ADT libraries were pooled in a 2:1 ratio and sequenced with an Illumina NovaSeq SP flow cell. Target sequencing depth for the GEX libraries was 20,000 read pairs per cell and 5,000 read pairs per cell for the ADT libraries.

value: CD34+ cells

value: Hematopoietic stem and progenitor cells

value: Granulocyte-colony stimulating factor or PBS

tag: antibodies/tags


title: Zebrafish_KO1

tag: genotype


title: P2_E01_530_mono_10

tag: cell type


title: human CD34+ cells, CITE-seq Surface

description:
10x Genomics
Surface

library_source: other

molecule: protein

value: The following TotalSeqB antibodies anti-CD38, anti-CD90, anti-CD45RA, anti-CD49f, Hashtag1, Hashtag2, Hashtag3, Hashtag 4, Hashtag 5, Hashtag 6


title: IMR90 anti-MBD3

city: Montreal

first: Moshe

last: Szyf

state: QC Quebec

address: 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology & Therapeutics

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Base calling was performed with RTA v3.4.4 . Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Paired-end FASTQ files were trimmed for quality and adapter content using Trim Galore v0.6.7 with default parameters.
Trimmed FASTQ files were aligned to hg38 reference genome using bowtie239 v2.4.5 with default parameters.
SAM files were converted to BAM format and unmapped reads were removed with samtools v1.16.1
BAM files were sorted and duplicates were marked with Picard tools v2.18.29 and indexed with samtools.
Significant peaks were identified with the callpeak function from macs2 v2.2.7.1 using the respective input sequencing data for each sample as control and precompiled values for the mappable human genome size.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for input samples)

growth_protocol: All cell lines were maintained in DMEM, high glucose (Thermo Fisher, cat. no. 11965118) supplemented with 10% fetal bovine serum (FBS) (Wisent, cat. no. 080-150) and 1X Penicillin-Streptomycin-Glutamine (Thermo Fisher, cat. no. 10378016) and grown in a 37 °C humidifed 5% CO2 incubator. Media was replaced or cells were passaged every 3 days.

extract_protocol:
150mm tissue culture dishes containing 90% confluent cells from each experimental condition were cross-linked and immunoprecipitated with the Active Motif ChIP-IT High Sensitivity Kit according to manufacturers instructions and using indicated antibodies. Samples were sonicated on the Bioruptor (Diagenode) in 1.5 mL Eppendorf tubes at high power for two 10-minute cycles of 30 seconds on and 30 seconds off, replacing warmed water with ice-cold water and minimal ice between each cycle. 25 µL of sonicated chromatin was purified according to ChIP-IT HS Kit protocol and quantified by NanoDrop. 30 µg input chromatin was used for immunoprecipitation.
Libraries were generated from 25 µL of fragmented DNA (range 100-300 bp) using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), as per the manufacturer’s recommendations. Adapters and PCR primers were purchased from Integrated DNA Technologies (IDT). Size selection was carried out using SparQ beads (QIAGEN) prior to PCR amplification (12 cycles). Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average fragment size was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized, pooled, and then denatured in 0.05 N NaOH and neutralized using HT1 buffer. The pool was loaded at 175 pM (HEK293 cells) or 200pM (mouse cortices) on a Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level.

treatment_protocol: Cells were untreated (for MBD3 ChIP) or stably expressing 3XFLAG-TDG-N140A-CD (for FLAG ChIP) from a lentiviral vector.

value: Normal lung fibroblasts

value: endogenous TDG

tag: chip antibody

value: MBD3 (abcam, ab157464)


title: GBM8401 cells (bio rep1)


title: P2_E01_530_mono_09


title: Lot179_D20_CM

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
MAP-RSeqversion 3.0 and theSTARtool were usedto align the raw RNA seq reads to the reference human genome build hg38
QC was performed by FastQC pre- and post-read trimming
The RNA paired end reads were aligned using the STAR aligner 2.6.1c
Gene counts were generated using subread featuerCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hiPSC Lot179

growth_protocol: Human induced pluripotent 2D stem cell (iPSC) cultures were maintained and expanded in mTeSR1 media and grown on Laminin-coated 60 mm culture plates. 3D iPSC cultures were grown in a 1:1 ratio mTeSR1/StemPro-ESC.

extract_protocol:
RNA was harvested using Zymo Research Corporation Direct-zol™ RNA MiniPrep kit (Zymo Research Corporation).
Library was prepared using theIllumina® TruSeq® Stranded Total RNA access kit

treatment_protocol: 3D iPSC cultures were treated with CHIR, followed by IWP-3 and Insulin in B27-based differentiation media. iPSC were maintained in differentiation media for 20 days.

value: hiPSC Lot179

value: cardiac lineage-cells

value: WT

value: cardiac differentiation

tag: time

value: Day 20


title: Lot200_D20_CM

source_name: hiPSC Lot200

value: hiPSC Lot200


title: Lot200_2D_iPSC

value: pluripotent stem cell

value: Day 0


title: Lot192_D20_CM

source_name: hiPSC Lot192

value: hiPSC Lot192


title: MCF7 anti-MBD3

value: Breast epithelial cancer


title: Lot179_2D_iPSC


title: Zebrafish_WT3

value: liver


title: Zebrafish_WT2


title: P2_E01_530_mono_08

value: monocytes

value: TUM

value: peripheral blood


title: HEPG2 anti-MBD3

value: Hepatocellular carcinoma


title: Zebrafish_WT1


title: P2_E01_530_mono_07


title: IMR90 input for FLAG-TDG-N140A-CD and MBD3

value: Normal lung fibroblasts

value: stably expressing 3XFLAG-TDG-N140A-CD


title: HEK293 TDGKO anti-MBD3

value: Human embryonic kidney

value: TDGKO

value: MBD3 (abcam, ab157464)


title: HEK293 anti-MBD3

value: endogenous TDG


title: HEK293 TDG-N140A anti-MBD3


title: P2_E01_530_mono_05


title: HEPG2 input for FLAG-TDG-N140A-CD and MBD3


title: Patient-derived fibroblast, sporadic ALS [S9]

city: San Francisco

first: Karl

last: Kumbier

address: 1700 4th Street, MC 2540

institute: University of California, San Francisco

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.
Reads were mapped to reference genome Homo sapiens GRCh38/hg38 using STAR 2.7.10a with default parameter settings.
Raw read counts were aggregated into a single (genes x samples) matrix of raw read counts.
Assembly: hg38
Supplementary files format and content: comma separated value file of raw read count values for all samples

growth_protocol: All fibroblast cell lines were cultured in DMEM/F-12 (Thermo Fisher Scientific, 11320-033) supplemented with 20% FBS (Gemini, Cat# COAA33H00I), 1% GlutaMAX (2 mM) and 1% Pen-Strep at 37deg C, 5% CO2 and 80% humidity.

extract_protocol:
Cells were harvested at around 1*10^6 (1mil)/mL, washed twice with PBS and stored at -80deg. RNA was harvested using RNeasy mini plus kit (Qiagen).RNA was thenmeasured by QuBit and NanoDrop to check quality and sent to Azenta for sequencing.
The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions.

value: Fibroblast

value: sporadic


title: IMR90 FLAG-TDG-N140A-CD

value: M2 Monoclonal ANTI-FLAG (Sigma, F1804)


title: Patient-derived fibroblast, sporadic ALS [S10]


title: Patient-derived fibroblast, sporadic ALS [S11]


title: Patient-derived fibroblast, sporadic ALS [S7]


title: P2_E01_530_mono_03


title: MCF7 input for FLAG-TDG-N140A-CD and MBD3


title: P2_E01_530_mono_04


title: MCF7 FLAG-TDG-N140A-CD


title: Patient-derived fibroblast, sporadic ALS [S8]


title: HEK293 input for FLAG-TDG-N140A-CD replicate 3


title: HEK293 input for FLAG-TDG-N140A-CD replicate 1


title: HEK293 input for FLAG-TDG-N140A-CD replicate 2


title: HEPG2 FLAG-TDG-N140A-CD


title: Patient-derived fibroblast, sporadic ALS [S6]


title: HEK293 anti-FLAG negative control (no FLAG-TDG)

value: no FLAG-TDG


title: HEK293 FLAG-TDG-N140A-CD replicate 3


title: P2_E01_530_mono_01


title: Patient-derived fibroblast, sporadic ALS [S5]


title: HEK293 FLAG-TDG-N140A-CD replicate 2


title: P2_E01_529_mono_64


title: APOBEC-sequencing of input for FLAG-TDG-N140A-CD replicate 3

data_processing:
Base calling was performed with RTA v3.4.4.
The program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Paired-end FASTQ files were trimmed for quality and adapter content using Trim Galore v0.6.7 with default parameters.
Reads were aligned to custom HEK293 (GRCh38) reference genomes using bismark v0.23.1 with default parameters. Custom HEK293 reference genome has the same chromosomal coordinates as GRCh38 and was built by merging all (non-converted) ChIP-seq alignments (associated with this dataset) from anti-FLAG-TDG/input samples, calling SNPs and INDELs with freebayes v1.3.6, filtering for SNPs with QUAL scores above 30 using vcffilter v1.0.3, and applying called SNPs (no INDELs) to the hg38 genome using the Genome Analysis Toolkit (GATK) v4.2.6.1 FastaAlternateReferenceMaker tool.
Bismark alignments were processed by Bismark deduplication and methylation extractor scripts.
Assembly: GRCh38
Supplementary files format and content: Bismark deduplicated coverage files.
Library strategy: APOBEC-seq

growth_protocol: Cell lines were maintained in DMEM, high glucose (Thermo Fisher, cat. no. 11965118) supplemented with 10% fetal bovine serum (FBS) (Wisent, cat. no. 080-150) and 1X Penicillin-Streptomycin-Glutamine (Thermo Fisher, cat. no. 10378016) and grown in a 37 °C humidifed 5% CO2 incubator. Media was replaced or cells were passaged every 3 days.

extract_protocol:
150mm tissue culture dishes containing 90% confluent cells from each experimental condition were cross-linked and immunoprecipitated with the Active Motif ChIP-IT High Sensitivity Kit according to manufacturers instructions and using indicated antibodies. Samples were sonicated on the Bioruptor (Diagenode) in 1.5 mL Eppendorf tubes at high power for two 10-minute cycles of 30 seconds on and 30 seconds off, replacing warmed water with ice-cold water and minimal ice between each cycle. 25 µL of sonicated chromatin was purified according to ChIP-IT HS Kit protocol and quantified by NanoDrop. 30 µg input chromatin was used for immunoprecipitation.
Libraries were generated from 200 ng fragmented input or 3.5-200 ng ChIP DNA using the NEBNext® Enzymatic Methyl-seq Kit (NEB, cat. no. E7120L) with some modifications to the manufacturer’s protocol. End prep and ligation of EM-seq adapter ligation were performed as per the manufacturer’s protocol except that the NEBNext EM-seq Adapter was substituted with 5hmC Adapter provided as a gift by NEB: this is critical as methylated NEBNext Em-seq Adapters included with the kit are not resistant to APOBEC-conversion alone. Cleanup after adapter ligation was performed with NEBNext Sample Purification Beads as per manufacturer’s protocol but elution volume was reduced to 17 µL for compatibility with the modified protocol. The TET2 oxidation step of the NEBNext® Enzymatic Methyl-seq Kit protocol was then skipped and 16 µL eluant was used directly for the APOBEC conversion (denaturation and deamination) steps. Denaturation with formamide, deamination with APOBEC, cleanup, PCR amplification, and final cleanup steps were performed according to the manufacturer’s protocol. Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized and pooled and then denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 200pM on a Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x150 cycles (HEK293 cells) or 2x100 cycles (mouse cortices) (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level.

treatment_protocol: Cells were stably expressing 3XFLAG-TDG-N140A-CD (for FLAG ChIP) from a lentiviral vector.


title: Patient-derived fibroblast, sporadic ALS [S4]


title: APOBEC-sequencing of input for FLAG-TDG-N140A-CD replicate 2


title: P2_E01_529_mono_63


title: P2_E01_530_mono_06


title: P2_E01_530_mono_02


title: APOBEC-sequencing of ChIP DNA for FLAG-TDG-N140A-CD, replicate 3


title: Patient-derived fibroblast, sporadic ALS [S2]


title: APOBEC-sequencing of ChIP DNA for FLAG-TDG-N140A-CD, replicate 1


title: P2_E01_529_mono_62


title: APOBEC-sequencing of ChIP DNA for FLAG-TDG-N140A-CD, replicate 2


title: P2_E01_529_mono_61


title: APOBEC-sequencing of input for FLAG-TDG-N140A-CD replicate 1


title: Patient-derived fibroblast, sporadic ALS [S1]


title: H1299 cells, siFOXN3-2, rep1

city: zhengzhou

first: XuDong

last: Li

address: 40 North University Road

department: Academy of Medical Science

institute: zhengzhou university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp version 0.14.0
Trimmed sequence reads were mapped to GRCh38 using hisat2 version 2.1.0
Reads mapped to the exon regions of each gene were counted byfeatureCounts StringTie version 1.3.3b and then FPKMs were calculated.
Assembly: GRCh38
Supplementary files format and content: files include FPKM values for each Sample

growth_protocol: H1299 cells were cultured in 5% CO2 at 37℃ and PRMI-1640 medium containing 10% FBS and 100 μg/mL penicillin and streptomycin were used

extract_protocol:
TRIzol reagent (Takara) was used to isolate total RNA.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: 50 nM siRNAs(siControl or siFOXN3-1 or siFOXN3-2) and transfection reagent (Lipofectamine RNAiMAX from Invitrogen) were added into OPTI-MEM respectively and mixed up after 5 minutes. The mixture were put into prepared human lung cancer cells with the density of 30%-50% 20 minutes later

value: epithelial-like cell derived from non-small cell lung cancer

value: FOXN3  knockdown

value: Transfect siFOXN3 by using the other RNAiMAX of the same type


title: H1299 cells, siFOXN3-2, rep3

value: Transfect siFOXN5 by using the other RNAiMAX of the same type


title: Patient-derived fibroblast, FUS-ALS [F12]

source_name: Patient-derived fibroblast, FUS-ALS

value: FUS; P525L


title: H1299 cells, siFOXN3-2, rep2

value: Transfect siFOXN4 by using the other RNAiMAX of the same type


title: P2_E01_529_mono_60

value: monocytes

value: TUM

value: peripheral blood


title: HEK293 FLAG-TDG-N140A-CD replicate 1

value: Human embryonic kidney

value: stably expressing 3XFLAG-TDG-N140A-CD


title: Patient-derived fibroblast, FUS-ALS [F11]

value: FUS; R521G


title: H1299 cells, siFOXN3-1, rep2

value: Transfect siFOXN3 by using RNAiMAX


title: H1299 cells, siFOXN3-1, rep3


title: H1299 cells, siFOXN3-1, rep1


title: P2_E01_529_mono_58


title: H1299 cells, siControl, rep3

value: WT

value: Transfect siControl by using RNAiMAX


title: P2_E01_529_mono_57


title: P2_E01_529_mono_59


title: H1299 cells, siControl, rep1


title: Patient-derived fibroblast, sporadic ALS [S3]

value: Fibroblast

value: sporadic


title: H1299 cells, siControl, rep2

value: epithelial-like cell derived from non-small cell lung cancer


title: Patient-derived fibroblast, FUS-ALS [F10]

value: FUS; H517Q


title: Patient-derived fibroblast, FUS-ALS [F9]


title: T_electroRNP_Donor3

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Basecalling using blc2fastq and trimming using cutadapt.
Alignment using STAR and gene abundance estimation using featurecounts.
Differential gene expression computed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: *.tsv: Tab-separated count files.

source_name: Peripheral Blood

extract_protocol:
Total RNA was isolated at 12-24 hours after editing using RNeasy Micro Kit (QIAGEN), and DNase treatment was performed using RNase-free DNase Set (QIAGEN), according to the manufacturer’s instructions.
RNA was quantified with The Qubit 2.0 Fluorometer (Thermo Fisher) and its quality was assessed by a 2100 Agilent Bioanalyser (Agilent Technologies). Minimum quality was defined as RNA integrity number (RIN) of >8. 20-100 ng of total RNA were used for library preparation and subsequent ultra-low input or standard sequencing by Genewiz (Azenta Life Sciences).

value: Peripheral Blood

value: CD4+ T cells

tag: donor

tag: disease status

value: Healthy

value: RNP

tag: replicate


title: P2_E01_529_mono_56

data_processing:
Smart-Seq2
Genome_build: mm10
Supplementary_files_format_and_content: counts

extract_protocol:
Cells were sorted into 96 well place containing 2 ul of lysis buffer in each well
as per Smart-seq2 protocol (Picelli et al 2013)
Nextera; 75bp + 75bp; HiSeq2500

value: monocytes


title: P2_E01_529_mono_55

value: TUM


title: Patient-derived fibroblast, FUS-ALS [F8]

value: FUS; R495X


title: T_LNPsRNA_Donor3

value: LNPs


title: T_emptyLNPs_Donor3

value: Empty LNPs


title: Patient-derived fibroblast, FUS-ALS [F7]

value: FUS; R521G


title: T_UT_Donor3

value: UT


title: T_electroRNA_Donor3

value: RNA


title: T_LNPsRNA_Donor2


title: P2_E01_529_mono_53

value: peripheral blood


title: Patient-derived fibroblast, FUS-ALS [F6]

value: Fibroblast

value: FUS; E516insD


title: T_emptyLNPs_Donor2


title: Patient-derived fibroblast, FUS-ALS [F5]

value: FUS; G522A


title: T_electroRNA_Donor2


title: P2_E01_529_mono_52


title: Patient-derived fibroblast, FUS-ALS [F3]


title: T_UTelectro_Donor3

value: Mock electro


title: Patient-derived fibroblast, FUS-ALS [F2]

value: FUS; P525L


title: T_UTelectro_Donor2

value: Peripheral Blood

value: CD4+ T cells


title: CY1

city: Yangzhou

first: Jing

last: Zhang

address: 48 Wenhui Road

institute: Yangzhou university

data_processing:
Illumina Novaseq 6000 platform used for basecalling.
Clean reads were obtained by removing adapters, high contents of unknown bases reads and low quality reads
The clean reads were mapped to the reference genome of Chinese white pear deposited in the GDR database (https://www.rosaceae.org/species/pyrus_bretschneideri/genome_v1.1)
Gene expression levels were estimated according to Fragments Per Kilobase of transcript sequence per Millions (FPKM)
Genome_build: Pyrus x bretschneideri (assembly Pbr_v1.1)
Supplementary_files_format_and_content: Excel files include genes read count and FPKM values for each sample (.xls)

organism: Pyrus pyrifolia

source_name: CuiYu

growth_protocol: Akibae, Nijisseiki,CuiYu and SuCui NO.1 pears were grew and harvested in orchards in Yizheng, Jiangsu, China;Chili pears were grew and harvested in an orchard in Yantai, Shandong, China

extract_protocol:
Total RNA was extracted by the ethyl ammonium bromide (CTAB) method using skin tissues collected from fruits with three biological replicates.
RNA-Seq library was generated with NEB Next® UltraTM RNA Library Prep Kit for Illumina (NEB, USA) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The fruits were harvested at maturity stage without treatment

tag: variety

value: CuiYu

value: pear fruit harvested at maturity stage (105 days after full bloom) without treatment

tag: organ

value: fruit skin


title: P2_E01_529_mono_54

value: monocytes

value: TUM


title: Lot192_2D_iPSC

value: hiPSC Lot192

value: pluripotent stem cell

value: WT

value: cardiac differentiation

value: Day 0


title: CY2


title: SC3

source_name: SuCui NO.1

value: SuCui NO.1


title: SC2


title: Patient-derived fibroblast, healthy control [H13]

value: Fibroblast


title: P2_E01_529_mono_48

value: peripheral blood


title: T_emptyLNPs_Donor1

value: Healthy

value: Empty LNPs


title: Patient-derived fibroblast, FUS-ALS [F1]

value: FUS; E516insD


title: SC1


title: T_LNPsRNA_Donor1

value: Peripheral Blood

value: CD4+ T cells

value: LNPs


title: Patient-derived fibroblast, healthy control [H12]


title: T_electroRNP_Donor2

value: RNP


title: Patient-derived fibroblast, FUS-ALS [F4]

value: FUS; R524W


title: P2_E01_529_mono_46

value: monocytes

value: TUM


title: T_electroRNA_Donor1

value: RNA


title: NS3

source_name: Nijisseiki

value: Nijisseiki

value: pear fruit harvested at maturity stage (135 days after full bloom) without treatment

value: fruit skin


title: P2_E01_529_mono_51


title: CY3

value: CuiYu

value: pear fruit harvested at maturity stage (105 days after full bloom) without treatment


title: P2_E01_529_mono_50

value: peripheral blood


title: P2_E01_529_mono_49


title: T_electroRNP_Donor1

value: Healthy


title: P2_E01_529_mono_45


title: T_UTelectro_Donor1

value: Mock electro


title: T_UT_Donor2

value: UT


title: Patient-derived fibroblast, healthy control [H10]

value: Fibroblast

value: WT


title: P2_E01_529_mono_44


title: P2_E01_529_mono_47


title: P2_E01_529_mono_42


title: AB3

source_name: Akibae

value: Akibae

value: pear fruit harvested at maturity stage (120 days after full bloom) without treatment


title: HSPC_LNPsRNA_Rep3

value: Peripheral Blood

value: HSPC

value: Pool

value: LNPs


title: Patient-derived fibroblast, healthy control [H9]


title: AB2


title: D7_IEL_1 [scRNA-seq]

tag: age

value: 6-16 Weeks

value: Small Intestine Epithelium

value: LCMV-Armstrong


title: Patient-derived fibroblast, healthy control [H11]


title: Patient-derived fibroblast, healthy control [H8]


title: P2_E01_529_mono_41

value: monocytes

value: TUM


title: Patient-derived fibroblast, healthy control [H6]


title: P2_E01_529_mono_40

value: peripheral blood


title: AB1

value: fruit skin


title: Patient-derived fibroblast, healthy control [H5]


title: PCHT52

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

country: France

institute: INRAE

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Data were processed using miRDeep2 package (2.0.0.8). The raw reads were firstly trimmed against Illumina adapters, then mapped to the Btau_5.0.1 genome assembly as miRBase v22.1 with the Mapper module. Precursors and mature miRNAs were identified using the miRDeep2 core module, miRDeep2.pl. Potential miRNAs were annotated accordingly against ortholog miRNAs in goat, sheep and humans (miRBase release 22.1). We used a miRDeep2 score ≥5 as a cut-off threshold.
The normalization and differential expression analysis of the known and predicted miRNAs were conducted with the DESeq2 R package v1.26,0
Assembly: UMD3.1

organism: Bos taurus

source_name: purified small RNA

extract_protocol: Small RNA-Seq librairies were generated from 10 to 20 ng of purified small RNA fraction using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer's instructions. The protocol takes advantage of the natural structure common to most microRNA molecules that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3' RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5' RNA adapter. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 15 sec at 72oC] x 13 or 16cycles; 10 min at 72oC) to create cDNA constructs. Amplified cDNA constructs of 20 to 40 nt were selectively isolated by acrylamide gel purification followed by ethanol precipitation.  The final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Healthy and Subclinical-Endometritis cows

value: blood serum

tag: animal id

tag: animal status

value: subclinical endometritis

tag: sample time point

value: day 45 of sampling


title: Patient-derived fibroblast, healthy control [H7]

tag: cell line

value: Fibroblast

value: WT


title: HSPC_electroRNA_Rep3

tag: tissue

value: Healthy

value: RNA


title: HSPC_electroRNP_Rep3

value: Peripheral Blood

value: HSPC

tag: treatment

value: RNP


title: NS1

value: Nijisseiki

value: pear fruit harvested at maturity stage (135 days after full bloom) without treatment


title: NS2


title: Patient-derived fibroblast, healthy control [H4]


title: P2_E01_529_mono_39

city: Edinburgh

first: Nizar

last: Batada

address: Crew Road

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

tag: strain


title: T_UT_Donor1

value: CD4+ T cells

value: UT


title: P2_E01_529_mono_43

value: monocytes

value: TUM


title: P2_E01_529_mono_38

value: peripheral blood


title: HSPC_UT_Rep3

value: Pool


title: Patient-derived fibroblast, healthy control [H3]

tag: genotype


title: HSPC_LNPsRNA_Rep2

tag: cell type

value: LNPs


title: PCHT50

value: blood serum

value: subclinical endometritis

value: day 45 of sampling


title: PCHT49

value: day 25 of sampling


title: HSPC_emptyLNPs_Rep3

value: Healthy

value: Empty LNPs


title: Patient-derived fibroblast, healthy control [H1]

value: Fibroblast

value: WT


title: P2_E01_529_mono_35


title: HSPC_electroRNA_Rep2

value: Peripheral Blood

value: HSPC

value: RNA


title: P2_E01_529_mono_34


title: HSPC_electroRNP_Rep2

value: RNP


title: P2_E01_529_mono_33

value: monocytes


title: HSPC_UTelectro_Rep3

value: Mock electro


title: PCHT51


title: PCHT46


title: PCHT45


title: PCHT48


title: HSPC_UT_Rep2

value: UT


title: P2_E01_529_mono_31

value: TUM

value: peripheral blood


title: P2_E01_529_mono_32


title: PCHT43

value: blood serum


title: HSPC_UTelectro_Rep2

value: Pool


title: PCHT44

value: subclinical endometritis

value: day 45 of sampling


title: P2_E01_529_mono_30


title: PCHT42


title: HSPC_LNPsRNA_Rep1

value: Healthy

value: LNPs


title: P2_E01_529_mono_36


title: HSPC_emptyLNPs_Rep1

value: Empty LNPs


title: Patient-derived fibroblast, healthy control [H2]

value: Fibroblast

value: WT


title: P2_E01_529_mono_29


title: P2_E01_529_mono_28


title: PCHT41

value: day 25 of sampling


title: HSPC_emptyLNPs_Rep2

value: Peripheral Blood

value: HSPC


title: PCHT47


title: PCHT40


title: HSPC_electroRNP_Rep1

value: RNP


title: P2_E01_529_mono_27

value: monocytes


title: P2_E01_529_mono_26


title: HSPC_UTelectro_Rep1

value: Mock electro


title: PCHT39


title: PCHT37


title: PCHT38


title: PCHT36


title: AAV6_Day12_Donor3

data_processing:
Basecalling using blc2fastq and trimming using cutadapt.
Alignment using STAR and gene abundance estimation using featurecounts.
Differential gene expression computed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Count_matrix.tsv: Tab-separated count file.

value: CD4+ T cells

value: AAV6 only

tag: time point

value: Day9 post treatment


title: P2_E01_529_mono_24

value: TUM

value: peripheral blood


title: P2_E01_529_mono_25


title: P2_E01_529_mono_23


title: P2_E01_529_mono_22


title: PCHT34

value: blood serum

value: subclinical endometritis

value: day 45 of sampling


title: PCHT35


title: RNP_Day12_Donor3

value: Healthy


title: H1975 NLS Mut 3

city: Los Angeles

first: Ze

last: Liu

address: 1441 Eastlake Ave. NOR 5306

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
Reads were mapped to GrCh38.p14 with STAR (v 2.7.9a) to generate counts
DESeq2 (v 1.36.0) was used to perform differential expression analysis
Assembly: GrCh38.p14
Supplementary files format and content: tab-delimited text files from STAR containing gene counts

source_name: lung adenocarcinoma

growth_protocol: H1975 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
TRI-Zol
Novogene

treatment_protocol: Cells were transfected with siRNA followed by transfection with expression plasmid of GRP78

value: lung adenocarcinoma

value: epithelial

value: NLS Mut

value: siRNA and plasmid


title: P2_E01_529_mono_21


title: H1975 NLS Mut 2


title: PCHT33

value: day 25 of sampling


title: RNP_AAV6_Day12_Donor3

value: Peripheral Blood

value: RNP + AAV6


title: H1975 NLS Mut 1


title: UT_electro_Day12_Donor3

value: Mock electro


title: PCHT32


title: UT_Day12_Donor3

value: CD4+ T cells

value: UT


title: H1975 WT 3

value: WT


title: AAV6_Day12_Donor2

value: AAV6 only

value: Day9 post treatment


title: PCHT31

value: blood serum


title: H1975 WT 2


title: P2_E01_529_mono_19

value: monocytes

value: TUM

value: peripheral blood


title: RNP_AAV6_Day12_Donor2

value: Healthy


title: P2_E01_529_mono_18


title: RNP_Day12_Donor2

value: RNP


title: H1975 WT 1

value: lung adenocarcinoma

value: epithelial


title: P2_E01_529_mono_17


title: PCHT24

value: healthy

value: day 45 of sampling


title: PCHT23

value: day 25 of sampling


title: P2_E01_529_mono_15


title: PCHT22


title: H1975 Vector 1

value: Vector

value: siRNA and plasmid


title: H1975 Vector 2


title: H1975 Vector 3


title: PCHT21


title: AAV6_Day12_Donor1

value: Peripheral Blood

value: CD4+ T cells


title: UT_Day12_Donor2

value: UT


title: HSPC_electroRNA_Rep1

value: HSPC

value: Pool

value: RNA


title: P2_E01_529_mono_20

value: monocytes

value: TUM


title: UT_electro_Day12_Donor2

value: Healthy

value: Mock electro

value: Day9 post treatment


title: RNP_AAV6_Day12_Donor1

value: RNP + AAV6


title: P2_E01_529_mono_14

value: peripheral blood


title: P2_E01_529_mono_16


title: HSPC_UT_Rep1


title: RNP_Day12_Donor1

value: RNP


title: P2_E01_529_mono_13


title: P2_E01_529_mono_12


title: UT_electro_Day12_Donor1


title: P2_E01_529_mono_11


title: PCHT18

value: blood serum

value: healthy

value: day 45 of sampling


title: PCHT17

value: day 25 of sampling


title: P2_E01_529_mono_10


title: PCHT19


title: PCHT16


title: AAV6_Day4_Donor3

value: Peripheral Blood

value: CD4+ T cells

value: AAV6 only

value: Day1 post treatment


title: P2_E01_529_mono_09


title: PCHT15


title: PCHT14


title: RNP_AAV6_Day4_Donor3


title: RNP_Day4_Donor3


title: PCHT13


title: P2_E01_529_mono_08


title: UT_electro_Day4_Donor3


title: P2_E01_529_mono_07


title: UT_Day4_Donor3

value: UT


title: P2_E01_529_mono_06

value: monocytes


title: si_88

city: Beijing

first: Yang

last: gu

address: 15 Datun Road

institute: institute of biophysics

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:
1) Remove the reads containing the adaptor(adaptor pollution);
2) Remove reads whose N content is greater than 5%;
3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Matrix table with raw gene counts and TPM values for each gene and each sample.

source_name: liver tumor

extract_protocol:
RNA was harvested using RNAprep Pure Micro Kit (Tiangen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using MGIEasy RNA Library Prep Kit V3.0 (MGI-tech) following manufacturer's protocols.

value: liver tumor

value: HCC Cell line

value: oncospheres

value: SNORD88B deficient


title: P2_E01_529_mono_05

value: TUM


title: si_NC

value: SNORD88B wild-type


title: AAV6_Day4_Donor2

value: Healthy


title: P2_E01_529_mono_04

value: peripheral blood


title: RNP_AAV6_Day4_Donor2

value: RNP + AAV6


title: phoU3

city: Bangkok

first: Tiyakhon

last: Chatnaparat

address: 50 Ngamwongwan Rd. Ladyao, Chatuchak

department: Plant Pathology

country: Thailand

institute: Kasetsart University

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Sequenced reads were trimmed for adaptor sequence, and then mapped to Xanthomonas citri pv.glycines 12-2 whole genome using Bioconductor Rsubread package with parameter align(index=" Xag12-2index ",readfile1="XagWT2_1.fastq.gz", readfile2="XagWT2_2.fastq.gz",output_file="WT2alignResults.BAM")
Genome_build: Xag12-2index
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample ...

organism: Xanthomonas citri pv. glycines

source_name: Bacterial cells

extract_protocol:
Total RNA from each strain was isolated using an RNeasy® Mini Kit (QIAGEN) and contaminating DNA was removed using TURBO DNA-free™ Kit (Ambion, Austin, TX, U.S.A.).
Libraries were prepared using Ribo-Zero rRNA Removal Kit (Bacteria), TruSeq RNA Sample Prep Kit v2 following the Illumina manufacturer’s instructions

value: Strain 12-2

value: phoU mutant


title: UT_Day12_Donor1

value: Peripheral Blood

value: Day9 post treatment


title: P2_E01_529_mono_03


title: RNP_Day4_Donor2

value: CD4+ T cells

value: RNP


title: UT_electro_Day4_Donor2

value: Mock electro

value: Day1 post treatment


title: phoB3

value: phoB mutant


title: HCC230pre

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95%

source_name: serum

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: Serum was collected from the blood.

extract_protocol: Total RNA from serum was extracted commercially available kit (miReasy mini kit (Qiagen)).

treatment_protocol: Blood was collected before surgical treatment.

tag: disease/diagnosis

value: hepatocellular carcinoma

tag: sample collection time

value: before operation

tag: molecule subtype

value: miRNA


title: phoB2


title: phoB1


title: HCC230post1

value: after operation within 14 days


title: UT_Day4_Donor2

tag: donor

tag: disease status

value: UT


title: RNP_AAV6_Day4_Donor1

value: Healthy


title: AAV6_Day4_Donor1

value: AAV6 only


title: WT3

value: wild-type


title: WT2

value: Strain 12-2


title: RNP_Day4_Donor1


title: UT_electro_Day4_Donor1


title: HCC226pre


title: phoU1

value: phoU mutant


title: WT1


title: HCC226post1


title: UT_Day4_Donor1

value: Peripheral Blood


title: HCC226post2

value: after operation beyand 14 days


title: HCC223post1


title: HCC223pre


title: HCC221pre


title: phoU2


title: UT_Day3_Donor3

value: CD4+ T cells

value: Pre treatment (Day 0)


title: UT_Day3_Donor2


title: UT_Day3_Donor1


title: HCC221post2


title: HCC218pre


title: OCI-AML2 Day21 Venetoclax-Ruxolitinib Rep2 [D21_VENRUX2_Ln2S6_L002]

city: Portland

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

institute: Oregon Health and Science University

description:
PCR library sequencing
LIB200527JT_AML2_D21_VENRUX2_Ln2S6_L002

data_processing:
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC  (Version 2.3)
Alignment: bowtie2 -p 1 -x yusa_library --xeq --norc -U {file}.trimmed.fastq {file}.tmp.sam (Version 2.3.5.1)
Conversion to BAM: samtools view -bS {file}.tmp.sam > {file}.bam (Version 1.9)
Filter to unique matches allowing no mismatches using bamtools (Version 2.5.1)
Counting reads for each sgRNA using MAGeCK: mageck count --norm-method none (Version: v0.5.8)
Assembly: Custom reference created from CRISPR library
Supplementary files format and content: Read counts per sgRNA for each sample

source_name: OCI-AML2 cells infected with library

growth_protocol: OCI-AML2 cells were grown in RPMI-1640, supplemented with 20% serum, L-glutamine, pen/strep, fungizone.

extract_protocol:
30 million cells were collected for each drug treatment in duplicate at day 14 and day 21. DNA was extracted by desalting method
50 micrograms of DNA were used to amplify sgRNA guide libraries using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)
Shalem et al Science 2014. 343(6166): p. 84-87

treatment_protocol: After transduction, puromycin (2 mg/ml final concentration) was applied  to each flask. After 7 days, cells were collected and resuspended in fresh media with either DMSO, venetoclax (0.5 uM) or venetoclax (0.1 uM) plus ruxolitinib (1 uM)

tag: genotype/variation

value: infected with CRISPR/Cas9 library

value: Day 21 post puromycin selection, Venetoclax-Ruxolitinib


title: OCI-AML2 Day21 Venetoclax-Ruxolitinib Rep1 [D21_VENRUX1_Ln2S5_L002]

description:
PCR library sequencing
LIB200527JT_AML2_D21_VENRUX1_Ln2S5_L002