20.109(S22):Class data

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20.109(S22): Laboratory Fundamentals of Biological Engineering

Sp17 20.109 M1D7 chemical structure features.png

Spring 2022 schedule        FYI        Assignments        Homework        Class data        Communication        Accessibility

       M1: Drug discovery        M2: Metabolic engineering        M3: Project design       


Module 1: Drug discovery

SDS-PAGE gel images

[SDS-PAGE dropbox folder]

small molecule selections

T/R

Team small molecule #1 (enter compound ID) small molecule #2 (enter compound ID) aggregation assay results
TR Red 83079118 69269200 https://www.dropbox.com/s/7eut5ymxmiel9rp/TR_teal_red.xlsx?dl=0
TR Orange 95877382 83023303 https://docs.google.com/spreadsheets/d/1Lr5QAYY-63bOfrxuzZh1hgpHfTkCcTuU/edit?usp=sharing&ouid=103020115084669070409&rtpof=true&sd=true
TR Yellow 69269200 83079118 https://www.dropbox.com/s/ssc6b9kp7h6s7zj/20.109%20T%3AR%20Yellow%20Team%20Aggregation%20Assay%20-%20Class%20Data.xlsx?dl=0
TR Green 69269200 83079118 https://www.dropbox.com/s/fzo02lfzgo5ujwk/20109_TR_Green_Aggregation_Assay_Data.pptx?dl=0
TR Blue 69269200 83079118 https://www.dropbox.com/s/ezfjb4xt84xv59e/TR_blue.xlsx?dl=0
TR Teal 69269200 83079118 https://www.dropbox.com/scl/fi/1cs77ilahj51l51cw0j2g/TR_Teal_83079119.xlsx?dl=0&rlkey=8l1cae481k6p7p5y8290e8pu2
TR Pink 69269200 83079118
TR Purple 69269200 83079118 https://www.dropbox.com/s/lsdcuxv3y863k3z/TR_purple%20aggregation%20results.xlsx?dl=0
TR Grey 69269200 83079118 https://docs.google.com/spreadsheets/d/12ZOkOtndcb5FXAd1vvHBD4weM_FrWICbkfcykoFhrGY/edit?usp=sharing
TR White 69269200 83079118 https://www.dropbox.com/scl/fi/8x98j2r2nfq2qgwr4eura/White-Team-Aggregation-Results.xlsx?dl=0&rlkey=varbpxlx0apo8b2zkdt4kbxev

W/F

Team small molecule #1 (enter compound ID) small molecule #2 (enter compound ID) aggregation assay results
WF Red 69269200 83079118 https://mitprod-my.sharepoint.com/:x:/g/personal/mrowlett_mit_edu/EXXtvBLjG9BLtZajiE1PqbUBBkSUVd5xolqzA2KO1u1ADg?e=JjooPh
WF Orange 83079118 69269200 https://www.dropbox.com/s/8ksmmtml3e673m5/WFOrange%20Aggregation%20Assay%20Data.xlsx?dl=0
WF Yellow 83079118 69269200 https://www.dropbox.com/scl/fi/cotyaashmbv0vrz7wfral/Aggregation-Analysis.xlsx?dl=0&rlkey=r3r8isia4mk6vmy29a5usdykq
WF Green 83079118 83023303 https://www.dropbox.com/s/u38arbolq8zn3xq/20220218_agg_assay_yellow_green%202.xlsx?dl=0
WF Blue 69269200 83079118 https://www.dropbox.com/scl/fi/zogoszln7ydo10em8b196/20220218_agg_assay_blue-83079118.xlsx?dl=0&rlkey=glixenu1uqfo6xa5t1fmvmi08
WF Pink 83079118 69269200 https://docs.google.com/spreadsheets/d/13URd1atEq8Aqa6Ur_RrGyESe3g_RDVHK/edit?usp=sharing&ouid=107012858600740729039&rtpof=true&sd=true
WF Purple 69269200 83079118 https://docs.google.com/spreadsheets/d/1WXBr83b12vb83pYv1bqTUPl5VGFIDap9uOjESwOH0tQ/edit?usp=sharing
WF White 69269200 83023303 https://www.dropbox.com/s/c2g5513td5fepee/Aggregation%20Data.xlsx?dl=0

Aggregation Results

[T/R Aggregation dropbox folder]


Localization Results

[Localization Dropbox folder]

Module 2: Metabolic engineering

Diagnostic Digest gels

[T/R diagnostic digest folder ]
[W/F Diagnostic Digest Folder]

sgRNA_target sequences

T/R

Team Ethanol (E) or Acetate (A) Gene targeted by CRISPRi gRNA gRNA (DNA) sequence (without tag at 3' end) Locus targeted (eg. beginning of gene, putative promoter, -35 region) Target coding or non-coding strand Ethanol / Acetate Assay Results
TR Red Acetate (A) aceE gagtttcgatcggatccacgtcatt beginning of gene target coding strand https://www.dropbox.com/scl/fi/im2nky48dz8dninn07pwk/TR_red_yield.xlsx?dl=0&rlkey=yhbf2t0sxdfmqxqkrrpc8hkah
TR Orange Ethanol (E) gltA gaacacaccttttgaaccgagagta beginning of gene target coding strand T/R data
TR Yellow Ethanol (E) pta-ack GTTTTTTTAGCCACGTATCAATTAT -35 region noncoding strand
TR Green Ethanol (E) aceE TTATTCCTTATCTATCTAATAACGT -30 region coding strand
TR Blue Acetate aceE GTCGCGAGTTTCGATCGGATCCACG beginning of gene coding strand https://www.dropbox.com/s/cxxrl6zmj2ckeiy/TR_Blue_M2D6_Acetate_Data.xlsx?dl=0
TR Teal Acetate aceE CGTCATTTGGGAAACGTTCT beginning of gene coding strand
TR Pink
TR Purple Ethanol pta GTAGGGATCAGCATAATAATAC beginning of gene non-template strand
TR Grey Ethanol aceE CGTCATTTGGGAAACGTTCTGACAT beginning of gene noncoding strand https://docs.google.com/spreadsheets/d/15mpS30zxthBy3nxzGolYUSkcbeGWi7QR/edit?usp=sharing&ouid=116057108253329472008&rtpof=true&sd=true
TR White Ethanol aceE AGTTTCGATCGGATCCACGTCATTT beginning of gene targeting the coding strand (Non template)

W/F

Team Ethanol (E) or Acetate (A) Gene targeted by CRISPRi gRNA gRNA (DNA) sequence (without tag at 3' end) Locus targeted (eg. beginning of gene, putative promoter, -35 region) Target coding or non-coding strand Colorimetric Assay Results
WF Red Ethanol (E) pta gaccgacgctggttccggta Beginning of coding sequence of gene Coding
WF Orange Ethanol (E) pta ttcgtagttcagagactgggcaaac beginning of gene coding
WF Yellow Ethanol (E) ppc CATTGCGTAGTAATGTCAGTATGC beginning of gene coding strand (non template)
WF Green Acetate (A) ppc CCCCAGACACCCCATCTTATCGTTT promoter coding strand (non template)
WF Blue Acetate (A) adhE ttcagcgacattagtaacagcc beginning of the gene coding strand (non-template)
WF Teal
WF Pink Ethanol (E) ldhA GTGATGTTGAATCACATTTAAGC -35 conding strand (non-template)
WF Purple Acetate (A) adhE gttcagcgacattagtaacagccat beginning of gene coding strand (non-template)
WF Grey
WF White Acetate (A) adhE ACAATTTATTAACTGTTAGCTATAA promoter (-10) non-coding strand (template)


Sequencing Data

[T/R sequencing files]

[W/F sequencing files]