| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | AA | AB | ||
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1 | Contact PI | Co-PI | Availability (or date avail) | Reagents, etc. | Description, etc. | Plasmids | Cells | Mice | Datasets | Libraries | Comments | Point of Contact email | Publication, PMID (if available) | ||||||||||||||||
2 | Breakefield | Breakefield | Y | lentivirus vectors expressing palmtdTomato and palm GFP | labels all membranes in cells and membranes of EVs; tdTomato is brighter than GFP version | Breakefield@hms.harvard.edu | PMC4437317 | ||||||||||||||||||||||
3 | Breakefield | Breakefield | lentivirus vector expressing membrane-bound Gaussia luciferase with a biotinylation signal both external to the membrane with an IRES GFP | Breakefield@hms.harvard.edu | |||||||||||||||||||||||||
4 | Breakefield | Breakefield | Y | lentivirus vector expressing humanized biotin ligase with a signal sequence -IRES-mCherry | labels all membranes in cells and membranes of EVs; when used in combination with the GlucB vector, the cells biotinylate the protein on the exterior labelling with streptavidin conjugates surface of the membrane allowing sensitive… | Breakefield@hms.harvard.edu | PMC393450 | ||||||||||||||||||||||
5 | Breakefield | Charest | DOX inducible lentivirus expressing palm GFP IRES Cre or Blast | labels plasma membrane and EVs upon dox administration; works in vitro and in vivo | acharest@bidmc.harvard.edu | ||||||||||||||||||||||||
6 | Breakefield | Charest | floxed F. luciferase transgenic mouse | acharest@bidmc.harvard.edu | |||||||||||||||||||||||||
7 | Breakefield | Charest | floxed EGFR and PDGFRa transgenic animals and their derivative glioblastoma cell lines | acharest@bidmc.harvard.edu | |||||||||||||||||||||||||
8 | Breakefield | Charest | DOX inducible lentivirus expressing miRNAs along with Cre or Blast | express miRNA of choice upon dox administration; works in vitro and in vivo | acharest@bidmc.harvard.edu | ||||||||||||||||||||||||
9 | Breakefield | Krichesvky | Y | glioblastoma exosome-associated small exRNA datasets | RNAseq libraries of exosomal RNA, including miRNA and other small RNA species; available within the publicly released exRNA Atlas | akrichevsky@rics.bwh.harvard.edu | |||||||||||||||||||||||
10 | Breakefield | Krichesvky | 2016-04-16 | FBS associated small RNA datasets | RNAseq libraries of exRNA found in commonly utilized FBS, including miRNA and other small RNA species | akrichevsky@rics.bwh.harvard.edu | 27503761 | ||||||||||||||||||||||
11 | Breakefield | Krichesvky | 2016-05-16 | glioblastoma RNP-associated small exRNA datasets | includes miRNA and other small RNA species | akrichevsky@rics.bwh.harvard.edu | |||||||||||||||||||||||
12 | Breakefield | Krichesvky | 2016-05-16 | glioblastoma extracellular long RNA datasets | includes mRNA and lncRNA | akrichevsky@rics.bwh.harvard.edu | |||||||||||||||||||||||
13 | Breakefield | Gould | Y; from SBI | pFF3 | Alix KO plasmid | Cas9-GFP-TK-Puro plasmid for mutating human Alix gene | sgould@jhmi.edu | ||||||||||||||||||||||
14 | Breakefield | Gould | Y; from SBI | pFF4 | CD63 KO plasmid | Cas9-GFP-TK-Puro plasmid for mutating human CD63 gene | sgould@jhmi.edu | ||||||||||||||||||||||
15 | Breakefield | Gould | Y; from SBI | pJM1084 | CD9 KO plasmid | Cas9-GFP-TK-Puro plasmid for mutating human CD9 gene | sgould@jhmi.edu | ||||||||||||||||||||||
16 | Breakefield | Gould | Y; from SBI | pJM1083 | HRS KO plasmid | Cas9-GFP-TK-Puro plasmid for mutating human HRS gene | sgould@jhmi.edu | ||||||||||||||||||||||
17 | Breakefield | Gould | Y; from SBI | pJM1086 | CD81 KO plasmid | Cas9-GFP-TK-Puro plasmid for mutating human CD81 gene | sgould@jhmi.edu | ||||||||||||||||||||||
18 | Breakefield | Gould | Y; from SBI | pJM1087 | syntenin KO plasmid | Cas9-GFP-TK-Puro plasmid for mutating human syntenin gene | sgould@jhmi.edu | ||||||||||||||||||||||
19 | Breakefield | Gould | Y | pJM920 | CMV-Acyl-mNeonGreen-2a-bleo | For expressing NeonGreen in microvesicles under bleomycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
20 | Breakefield | Gould | Y | pJM921 | CMV-AcylTyA-mNeonGreen-2a-bleo | For expressing NeonGreen in exosomes under bleomycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
21 | Breakefield | Gould | Y | pJM926 | CMV-Acyl-mNeonGreen-2a-bsd | For expressing NeonGreen in microvesicles under blasticidin selection | sgould@jhmi.edu | ||||||||||||||||||||||
22 | Breakefield | Gould | Y | pJM927 | CMV-AcylTyA-mNeonGreen-2a-bsd | For expressing NeonGreen in exosomes under blasticidin selection | sgould@jhmi.edu | ||||||||||||||||||||||
23 | Breakefield | Gould | Y | pJM932 | CMV-Acyl-mNeonGreen-2a-hyg | For expressing NeonGreen in microvesicles under hygromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
24 | Breakefield | Gould | Y | pJM933 | CMV-AcylTyA-mNeonGreen-2a-hyg | For expressing NeonGreen in exosomes under hygromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
25 | Breakefield | Gould | Y | pJM938 | CMV-Acyl-mNeonGreen-2a-puro | For expressing NeonGreen in microvesicles under puromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
26 | Breakefield | Gould | Y | pJM939 | CMV-AcylTyA-mNeonGreen-2a-puro | For expressing NeonGreen in exosomes under puromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
27 | Breakefield | Gould | Y | pJM1010 | CMV-Acyl-EGFP-2a-bleo | For expressing EGFP in microvesicles under bleomycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
28 | Breakefield | Gould | Y | pJM1019 | CMV-AcylTyA-EGFP-2a-bleo | For expressing EGFP in exosomes under bleomycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
29 | Breakefield | Gould | Y | pJM1014 | CMV-Acyl-EGFP-2a-hyg | For expressing EGFP in microvesicles under hygromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
30 | Breakefield | Gould | Y | pJM1020 | CMV-AcylTyA-EGFP-2a-hyg | For expressing EGFP in exosomes under hygromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
31 | Breakefield | Gould | Y | pJM1003 | CMV-Acyl-EGFP-2a-puro | For expressing EGFP in microvesicles under puromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
32 | Breakefield | Gould | Y | pJM1021 | CMV-AcylTyA-EGFP-2a-puro | For expressing EGFP in exosomes under puromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
33 | Breakefield | Gould | Y | pJM903 | CMV-Acyl-tdTomato*-2a-bleo | For expressing tdTomato in microvesicles under bleomycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
34 | Breakefield | Gould | Y | pJM917 | CMV-AcylTyA-tdTomato*-2a-bleo | For expressing tdTomato in exosomes under bleomycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
35 | Breakefield | Gould | Y | pJM907 | CMV-Acyl-tdTomato*-2a-bsd | For expressing tdTomato in microvesicles under blasticidin selection | sgould@jhmi.edu | ||||||||||||||||||||||
36 | Breakefield | Gould | Y | pJM923 | CMV-AcylTyA-tdTomato*-2a-bsd | For expressing tdTomato in exosomes under blasticidin selection | sgould@jhmi.edu | ||||||||||||||||||||||
37 | Breakefield | Gould | Y | pJM911 | CMV-Acyl-tdTomato*-2a-hyg | For expressing tdTomato in microvesicles under hygromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
38 | Breakefield | Gould | Y | pJM929 | CMV-AcylTyA-tdTomato*-2a-hyg | For expressing tdTomato in exosomes under hygromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
39 | Breakefield | Gould | Y | pJM915 | CMV-Acyl-tdTomato*-2a-puro | For expressing tdTomato in microvesicles under puromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
40 | Breakefield | Gould | Y | pJM935 | CMV-AcylTyA-tdTomato*-2a-puro | For expressing tdTomato in exosomes under puromycin selection | sgould@jhmi.edu | ||||||||||||||||||||||
41 | Breakefield | Gould | Y | pFF9 | CAG-lox-tdTomato-lox-AcylTyA-mNeonGreen-2a-NLSmTagBFP2-2a-puro | For expressing tdTomato prior to Cre expression, and exosomal NeonGreen (and nuclear BFP2) after Cre expression | sgould@jhmi.edu | ||||||||||||||||||||||
42 | Breakefield | Gould | Y | pFF9/attBattB | attB-CAG-lox-tdTomato-lox-AcylTyA-mNeonGreen-2a-NLSmTagBFP2-2a-puro-attB | For making tranagenic mice with the following inserted at the Rosa26 locus: CAG-lox-tdTomato-lox, followed by exosomal mNeonGreen and nuclear mTagBFP2 | sgould@jhmi.edu | ||||||||||||||||||||||
43 | Breakefield | Gould | Y | pJM770-pJM900 | more than 100 plasmids designed to target selected mRNAs to exosomes and/or microvesicles | For selective targeting of mRNAs to exosomes | sgould@jhmi.edu | ||||||||||||||||||||||
44 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for CD63 (verified by mutation screening and loss of protein by IB) | human cell line lacking CD63; currently being used to assess the role of CD63 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
45 | Breakefield | Gould | Y; from SBI | 293T cell lines deleted for CD63 (verified by mutation screening and loss of protein by IB) | Currently being used to assess the role of CD63 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
46 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for CD9 (verified by mutation screening and loss of protein by IB) | human cell line lacking CD9; currently being used to assess the role of CD9 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
47 | Breakefield | Gould | Y; from SBI | 293T cell lines deleted for CD9 (verified by mutation screening and loss of protein by IB) | human cell line lacking CD9; currently being used to assess the role of CD9 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
48 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for CD81 (verified by mutation screening and loss of protein by IB) | human cell line lacking CD81; currently being used to assess the role of CD81 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
49 | Breakefield | Gould | Y; from SBI | 293T cell lines deleted for CD81 (verified by mutation screening and loss of protein by IB) | human cell line lacking CD81; currently being used to assess the role of CD81 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
50 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for CD9 and CD81 (verified by mutation screening and loss of protein by IB) | human cell line lacking CD9 and CD81; currently being used to assess the role of CD9 and CD81 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
51 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for Alix (verified by mutation screening and loss of protein by IB) | human cell line lacking Alix; currently being used to assess the role of Alix in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
52 | Breakefield | Gould | Y; from SBI | 293T cell lines deleted for Alix (verified by mutation screening and loss of protein by IB) | human cell line lacking Alix; currently being used to assess the role of Alix in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
53 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for HRS (verified by mutation screening and loss of protein by IB) | human cell line lacking HRS; currently being used to assess the role of HRS in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
54 | Breakefield | Gould | Y; from SBI | 293T cell lines deleted for HRS (verified by mutation screening and loss of protein by IB) | human cell line lacking HRS; currently being used to assess the role of HRS in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
55 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for Rab35 (verified by mutation screening and loss of protein by IB) | human cell line lacking Rab35; currently being used to assess the role of Rab35 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
56 | Breakefield | Gould | Y; from SBI | 293T cell lines deleted for Rab35 (verified by mutation screening and loss of protein by IB) | human cell line lacking Rab35; currently being used to assess the role of Rab35 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
57 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for ARF6 (verified by mutation screening and loss of protein by IB) | human cell line lacking ARF6; currently being used to assess the role of ARF6 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
58 | Breakefield | Gould | Y; from SBI | 293T cell lines deleted for ARF6 (verified by mutation screening and loss of protein by IB) | human cell line lacking ARF6; currently being used to assess the role of ARF6 in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
59 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for Rab11a (verified by mutation screening and loss of protein by IB) | human cell line lacking Rab11a; currently being used to assess the role of Rab11a in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
60 | Breakefield | Gould | Y; from SBI | 293T cell lines deleted for Rab11a (verified by mutation screening and loss of protein by IB) | human cell line lacking Rab11a; currently being used to assess the role of Rab11a in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
61 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for Rab11a and Rab11b (verified by mutation screening and loss of protein by IB) | human cell line lacking Rab11a and Rab11b; currently being used to assess the role of Rab11a and Rab11b in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
62 | Breakefield | Gould | Y; from SBI | 293T cell lines deleted for Rab11a and Rab11b (verified by mutation screening and loss of protein by IB) | human cell line lacking Rab11a and Rab11b; currently being used to assess the role of Rab11a and Rab11b in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
63 | Breakefield | Gould | Y; from SBI | HEK293 cell lines deleted for syntenin (verified by mutation screening and loss of protein by IB) | human cell line lacking syntenin; currently being used to assess the role of syntenin proteins in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
64 | Breakefield | Gould | Y; from SBI | 293T cell lines deleted for syntenin (verified by mutation screening and loss of protein by IB) | human cell line lacking syntenin; currently being used to assess the role of syntenin proteins in the biogenesis of EVs, and in the biogenesis of exRNA (collaboration with Balaj & Breakefield) | sgould@jhmi.edu | |||||||||||||||||||||||
65 | Breakefield | Gould | not yet available | b6 mouse with the following integrated at the Rosa26 locus: CAG-lox-tdTomato-lox-AcylTyA-mNeonGreen-2a-NLSmTagBFP2-2a-puro | Cre-responsive mouse (b6) that (a) expresses cytoplasmic tdTomato in all cells, and (b) switches to exosomal NeonGreen (and nuclear blue expression) after Cre expression | For generating a map of exosome traffic in the mouse; map will be generated by a combination of (i) transplant studies and (ii) Cre activation studies, with the goal of identifying a map of exosome trafficking in the body | sgould@jhmi.edu | ||||||||||||||||||||||
66 | McManus | McManus | Y | Sensor cell constructs that report on exRNA activity | Sensor constructs are in the form of lentiviruses and can detect a number of different microRNAs in cell lines. IDG cooperative members are welcome to request vectors as libraries or titered lentivirus. Information related to vectors is available upon request. | Michael.McManus@ucsf.edu | unpublished | ||||||||||||||||||||||
67 | McManus | McManus | Y | CRISPR constructs | IDG cooperative members are welcome to request vectors as libraries or titered lentivirus. Information related to vectors is available upon request. | Michael.McManus@ucsf.edu | unpublished | ||||||||||||||||||||||
68 | McManus | McManus | Y | Sensor cell lines that report on exRNA activity | Michael.McManus@ucsf.edu | unpublished | |||||||||||||||||||||||
69 | McManus | McManus | Y | some CRISPR transgenic cell lines | Michael.McManus@ucsf.edu | unpublished | |||||||||||||||||||||||
70 | McManus | McManus | Y | exRNA KO mice | We have excellent protocols and can make the mice for you. Mouse reagents can be provided by shipping animals or ES cells or possibly sperm. | Michael.McManus@ucsf.edu | unpublished | ||||||||||||||||||||||
71 | McManus | McManus | Y | High titer lentivirus | We can make high titer lentivirus in our Core. | Michael.McManus@ucsf.edu | unpublished | ||||||||||||||||||||||
72 | McManus | McManus | Y | a number of different microRNA KO mice | Mouse reagents can be provided by shipping animals or ES cells or possibly sperm. | Michael.McManus@ucsf.edu | unpublished | ||||||||||||||||||||||
73 | McManus | McManus | Y | Pooled whole genome human shRNA library. | Libraries are broken up into subpools. For RNAi, 25-30 shRNA against every Refseq human gene. 600K shRNAs total. | Michael.McManus@ucsf.edu | unpublished | ||||||||||||||||||||||
74 | McManus | McManus | Y | Pooled whole mouse and human genome CRISPR libraries for editing, CRISPRi, and CRISPRa. | Libraries are broken up into subpools. For sgRNAs, 12 sgRNAs/gene for every Refseq gene. | Michael.McManus@ucsf.edu | unpublished | ||||||||||||||||||||||
75 | McManus | Voinnet | happy to share reagents via collaboration (will evolve with publication status) | miRNA sensor cell line in a miRNA WT or KO context (using McManus pOSIsensor system) | The pOSI-sensor lines were generated from different parental cell lines including 293T (embryonic carcinoma), RKO (colon cancer) and C2C12 (mouse myoblast). So far, we have mostly developed sensors against miR-21 and miR-22. pOSI-sensors are currently being introduced in other cell types. | bogdanm@ethz.ch | unpublished | ||||||||||||||||||||||
76 | McManus | Voinnet | happy to share reagents via collaboration (will evolve with publication status) | Cell lines stably expressing RNA silencing factors (e.g. Dicer, Drosha, AGO2...) | Concerning the RNA silencing factors: we have generated a collection of plasmids coding for either N- or C-terminally tagged DGCR8, DROSHA, XPO5, DICER1, TARBP2, PACT, AGO1, and AGO2. The tag consists of flag-SBP-mNeonGreen. Red (mRuby2) or Blue (mTAGBF2) N-terminal tags are also available. Flag and SBP can be used as affinity tags for immunoprecipitation (e.g. IP-MS). The plasmid backbone is pCDNA5/FRT/TO, allowing easy generation of stable isogenic cell lines using the Flp-in system (Invitrogen). We have already generated stable lines in different parental cell lines including 293T, DLD1, C2C12, Neuro2A, and U2OS. | bogdanm@ethz.ch | unpublished | ||||||||||||||||||||||
77 | McManus | Voinnet | happy to share reagents via collaboration (will evolve with publication status) | Cell lines allowing a reversible association of tagged RNA silencing factors with specific endomembrane compartments (ER, Golgi, MVB) | Concerning the RNA silencing factors: we have generated a collection of plasmids coding for either N- or C-terminally tagged DGCR8, DROSHA, XPO5, DICER1, TARBP2, PACT, AGO1, and AGO2. The tag consists of flag-SBP-mNeonGreen. Red (mRuby2) or Blue (mTAGBF2) N-terminal tags are also available. Flag and SBP can be used as affinity tags for immunoprecipitation (e.g. IP-MS). The plasmid backbone is pCDNA5/FRT/TO, allowing easy generation of stable isogenic cell lines using the Flp-in system (Invitrogen). We have already generated stable lines in different parental cell lines including 293T, DLD1, C2C12, Neuro2A, and U2OS. | bogdanm@ethz.ch | unpublished | ||||||||||||||||||||||
78 | McManus | Voinnet | happy to share reagents via collaboration (will evolve with publication status) | Mouse models allowing cell-type specific expression of GFP-AGO2 or membrane-bound fluorescent protein in mammary gland (e.g. milk secretion) or intestine cells. | These mice make it possible to track AGO2 or vesicles secreted from these two differents organs. | bogdanm@ethz.ch | unpublished | ||||||||||||||||||||||
79 | McManus | Hunter | happy to share reagents via collaboration (will evolve with publication status) | SidT1 and SidT2 KO mice | Craig_Hunter@harvard.edu | ||||||||||||||||||||||||
80 | Tuschl | Tuschl | exRNA and exDNA isolation protocols including formulations of all individual components for urine/plasma/serum | Patented process to fractionate exRNA and exDNA using manuel or robotic process starting with 500 µl biofluid and recovering near 10 ng nucleic acid in 15 µl water in high purity suitable for enzymatic cDNA library preparation; processing of up to 200 samples/day is possible, method tested on about 1000 samples of urine and plasma | Detailed protocols are availabe, but they have not been posted on public web sites to not compromise publication. We are preparing a manuscript to be submitted soon | Klaas Max: Klaas.Max@rockefeller.edu; Thomas Tuschl: ttuschl@rockefeller.edu | |||||||||||||||||||||||
81 | Tuschl | Tuschl | Small RNA cDNA library preparation protocols for parallel processing of 24 samples with 5 ng input exRNA followed by Illumina 50 nt single end sequencing | Process originally developed for miRNA discovery and dependent on 5' phophate/3' hydroxyl termini. Provides 10-100-fold enrichment for RNA with such termini (miRNAs, 5' ends of tRNAs and Y RNAs). Used pre-adenylated bar-coded 3' adapter ligation to initaite sample processing, subsequent pooling, 5' adapter ligation, size fractionation, then cDNA synthesis, PCR and sequencing of barcoded 24 samples per lane. | Detailed protocols are availabe, but the latest addition of barcoded adapters has not been published. Hafner M, Renwick N, Farazi TA, Mihailović A, Pena JT, Tuschl T, Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing, Methods. 2012, 58, 164-70. This paper describes a set of 20 adapters and uses larger quantities of input RNA; updates to the protocol will be published with the RNA/DNA isolation manuscript in March 2016 | Klaas Max: Klaas.Max@rockefeller.edu; Thomas Tuschl: ttuschl@rockefeller.edu | |||||||||||||||||||||||
82 | Tuschl | Tuschl | Computational analysis of small RNAseq data using hierarchical mapping against a curated coding and ncRNA human transcriptome | These protocols have not been fully tested, they are under development. No manuscript yet in preparation | Klaas Max: Klaas.Max@rockefeller.edu; Thomas Tuschl: ttuschl@rockefeller.edu | ||||||||||||||||||||||||
83 | Tuschl | Beatrice Goilav, Zev Williams | Collection of cell-free blood and urine samples from people of lupus subtypes (nephritis, erythematosus) and of normal controls. Immortalized B-cell lines from lupus patients | Protocols for standardized biofluid collections. Protocols for Epstein Barr-Virus-based immortalization of leukocytes | Self-explanatory. Details best discussed in person. | bgoilav@montefiore.org, zwilliams@rockefeller.edu | |||||||||||||||||||||||
84 | Tuschl | Dinshaw Patel | Structural determination of protein-nucleic acid complexes by X-ray crystallogrphay and molecular characteriation of protein-nucleic acid complexes using biophysical methods | Structural characterization of riboswitches and DNA- and RNA-sensing innate immunity proteins; no specific approaches for exRNA transport or biogenesis | Self-explanatory. Details best discussed in person. | pateld@MSKCC.ORG | |||||||||||||||||||||||
85 | Blelloch | Mark Ansel | happy to share via collaboration | Ago1/Ago2 conditional mutant mice (Eif2c1tm1a(KOMP)Wtsi x Eif2c2tm1.1Tara) | Ago1 allele generated using the KOMP/EUCOMM targeting strategy described as knockout-first allele: Promoterless selection cassette. http://www.knockoutmouse.org/about/targeting-strategies. Live mouse colony currently in stock and intercrossed with Ago2fl/fl allele from the Tarakhovsky group at The Rockefeller University. | Mark.Ansel@ucsf.edu | Bronevetsky Y et al. J Exp Med 210(2):417-32 PMID: 23382546 | ||||||||||||||||||||||
86 | Blelloch | Mark Ansel | happy to share via collaboration | Conditional epitope tagged Ago2 transgenic mice (Gt(ROSA)26Sortm1(CAG-GFP/Eif2c2)Zjh) crossed to Ago2 conditional knockout mice | Previously published transgenic mouse bearing floxed STOP, GFP and myc tagged Ago2 under the control of the CAG promoter in the ROSA26 locus. Cre-mediated removal of a floxed STOP sequence allows expression of the GFP/myc tagged Ago2, with GFP expression indicating expression of Ago2 and the myc epitope tag allowing affinity purification of associated miRNAs. Live mouse colony currently in stock and intercrossed with Ago2fl/fl allele from the Tarakhovsky group at The Rockefeller University. | Mark.Ansel@ucsf.edu | unpublished intercross. Original mice in PMID 22243745 and PMID 17626790 | ||||||||||||||||||||||
87 | Blelloch | Robert Blelloch | happy to share via collaboration | RWPE myr-AKT (untransformed prostate epithelial line overexpressing myr-AKT) | Oncogene introduced as a retrovirus and purified by puro selection. | Robert.Blelloch@ucsf.edu | unpublished | ||||||||||||||||||||||
88 | Blelloch | Robert Blelloch | happy to share via collaboration | RWPE HRasV12 (untransformed prostate epithelial line overexpressing HRas V12) | Oncogene introduced as a retrovirus and purified by puro selection. | Robert.Blelloch@ucsf.edu | unpublished | ||||||||||||||||||||||
89 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A MYC 5X cells (human MYC over-expression ~ 5-fold by western blot) | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
90 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A myr-AKT (cells over-expressing myr-AKT) | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
91 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A AURKB (cells stably over-expressing Aurora Kinas B) | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
92 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A HRAS V12 expression | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
93 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A activated beta-catenin stable expression | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
94 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A NOTCH (activated Notch intracellular domain overexpression) | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
95 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A Puro / Blast control cells | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
96 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A Src-ER (conditional SRC activation) | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
97 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A BRAF V600E activated allele | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
98 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A PIK3CA activated allele stabkle over-expression | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
99 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A CCND1 Overexpression | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
100 | Blelloch | Andrei Goga | cells happy to share; gene expression data happy to share via collaboration | MCF10A NeuNT stable overexpression | Andrei.Goga@ucsf.edu | PMCID: PMC4407699 | |||||||||||||||||||||||
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