Chip Key

Chip Experiment Key

Coded name: Exp1
Experiment number:1, 2
Chip version:Rosetta 10932/10934/11431/11432/11433
Description of experiment: fem-1(hc17) vs fem-3(q23)
Red RNA:fem-3(q23)
Green RNA:fem-1(hc17)
Experimental details: fem-1(hc17) is a temperature sensitive loss-of-function mutation which, at 25 degrees Celsius, produces only oocytes and no sperm. Female soma and germline. fem-3(q23) is a temperature sensitive gain-of-function mutation which, at 25 degrees C, continually produces spermatids. Soma is female, germline is male. Both are fertile at 15 degrees.
Growth conditions: Synchronized populations of worms were grown at 15C on15cm enriched peptone agar plates seed with E.Coli. Worms were purified by pouring over a Nytex filter. Total RNA was isolated using the glass bead extraction protocol. Poly(A)+ RNA was isolated using the Invitrogen FastTrack 2.0 kit.
Comments:
Contact name: Sam Ward, University of Arizona

Coded name:Exp2
Experiment number:1
Chip version:Rosetta #10940
Description of experiment:unc-54::human B amyloid with mtl-2::GFP marker (CL2120) vs unc-54 plasmid with mtl-2::GFP marker (CL2122)
Red RNA:CL2120
Green RNA:CL2122
Experimental details:
Growth conditions:
Comments:
Contact name:Amy Fluet/Chris Link, University of Colorado

Coded name:Exp3
Experiment number:1
Chip version:Rosetta #10941
Description of experiment:unc-54::human B amyloid with rol-6 marker (CL2006) vs unc-54 plasmid with rol-6 marker (CL2099)
Red RNA:CL2006
Green RNA:CL2099
Experimental details:
Growth conditions:
Comments:
Contact name:Amy Fluet/Chris Link, Un. of Colorado

Coded name: Exp4
Experiment number: 1
Chip version: Rosetta #10939
Description of experiment: par-1 strain kk822 vs N2
Red RNA: N2
Green RNA: par-1 strain kk822
Experimental details: par-1strain kk822 is a temp sensitive strain that makes lots of pharynx.
Growth conditions: par-1 prep: Liquid cultures were grown as were N2 except the worms were grown at 15 degrees (the permissive temp) instead of room temp. Once the cultures had cleared the embryos were harvested as were the N2 except the solutions were kept cold to prevent "heat shocking" the temperature sensitive embryos. The embryos were plated on 150mm worm plates lacking food and allowed to hatch into L1's. Since par-1 does not have a post embryonic requirement the L1's were transferred to liquid cultures at 25 degrees (the non permissive temperature) and grown until the culture contained gravid adults. Embryos were collected and all should exhibit the par-1 phenotype of excess pharyngeal cells. Total RNA was extracted and poly A selected using the promega polytract kit.
Comments: These samples were sent to us pre-labelled with the Cy-dyes in 250 uL volume for each. 5 ug poly A+ RNA was used. Labelled cDNA was stored at -20 deg C for >3 months and was stable.
Contact name: Mike Horner/Susan Mango

Coded name: Exp5
Experiment number: 1,2,3
Chip version: Rosetta #10942, #10943, #10944
Description of experiment: tra-2(e2544ts);xol-1(y1) vs N2
Red RNA: N2 (A, B, C)
Green RNA: tra-2(e2544ts);xol-1(y1) (A, B, C)
Experimental details: A, B worms grown with antibiotics. C worms grown without antibiotics.
Growth conditions: Grown from liquid culture at 15 degrees from dauers; >eggs isolated and shifted to 25 degrees, and harvested at 15 hrs after >feeding. L2 stage.
Comments:pen/strep and nystatin in cultures
Contact name: David Zarkower

Coded name: Exp6
Experiment number: 1,2
Chip version: Rosetta #10945, #11489
Description of experiment: skn-1 (zu67)/Dnt1[unc?; let?] strain EU1 vs par-1 strain kk822
Red RNA: skn-1 (zu67)/Dnt1[unc?; let?] strain EU1
Green RNA: par-1 strain kk822
Experimental details:par-1 is a temp sensitive strain that makes lots of pharynx. skn-1 lacks pharynx cells.
Growth conditions:For par-1 prep see Exp4. skn-1 prep: Liquid cultures were grown at room temperature. Gravid adults were rinsed of bacteria and debris with M9 and plated on 150mm worm plates that had OP50 seeded on about 1/3 of the plate. Small aliquots of adult worms were spotted away from the food. Two populations of worms will be present. skn-1/Dnt1 heterozygotes and skn-1/skn-1 homozygotes. skn-1/Dnt1 worms are paralyzed because Dnt1 contains a dominant unc so these worms cannot reach the food. In contrast, skn-1/skn-1 adults are nonuncs and can crawl to the food source thus separating out the two differnt genotypes. After 2-4 hours the homozygous skn-1 adults were washed off the food containing side of the plate and bleached as before to collect the homozygous skn-1 embryos. Total RNA was extracted and poly A selected using the promega polytract kit.
Comments:These samples were sent to us pre-labelled with the Cy-dyes in 250 uL volume for each. 5 ug poly A+ RNA was used. Labelled cDNA was stored at -20 deg C for >3 months and was stable.
Contact name:Mike Horner/Susan Mango

Coded name: Exp7
Experiment number:1
Chip version:Rosetta # 10946
Description of experiment: skn-1 (zu67)/Dnt1 [unc?; let?] strain EU1 vs N2
Red RNA: N2
Green RNA: skn-1 (zu67)/Dnt1 [unc?; let?] strain EU1
Experimental details:skn-1 lacks pharynx cells.
Growth conditions: see Exp6
Comments:These samples were sent to us pre-labelled with the Cy-dyes in 250 uL volume for each. 5 ug poly A+ RNA was used. Labelled cDNA was stored at -20 deg C for >3 months and was stable.
Contact name:Mike Horner/Susan Mango

Coded name: Exp8
Experiment number: 1
Chip version:Rosetta #10949
Description of experiment:GL108[age-1(rf14)] vs GL108[age-1(rf14)] heat shocked
Red RNA:GL108[age-1(rf14)] heat shock
Green RNA:GL108[age-1(rf14)]
Experimental details:GL108[age-1(rf14)] worms grown at 20 degrees C . The heat shocked worms were grown at 20, submitted to HS 2 hours at 35 degrees C, followed by a 2h recovery at 20 deg.
Growth conditions:
Comments:
Contact name: Gordon Lithgow/David Walker

Coded name: Exp9
Experiment number: 1, 2, 3
Chip version:Rosetta #10952, #11435, #11482
Description of experiment:DP1,DP2, DP3 vs mec-3 amplicon
Red RNA: DP1, DP2, mec-3
Green RNA: mec-3 amplicon for first 2 exp, and DP3
Experimental details: DP1 is the difference product generated after 3 rounds of subtraction and PCR by using cDNA from N2 as tester and cDNA from 3 different mec-3 nonsense mutants as driver. Both DP1 and mec-3 amplicon are labeled by nick translation.
Growth conditions: Worms are gownn at 25 degree on agarose plates for about 3 generations before the harvest and RNA prep.
Comments:
Contact name:Marty Chalfie/ Yun Zhang, Department of Biological Science, Columbia University, NY

Coded name:Exp10
Experiment number:1
Chip version: Rosetta #10950
Description of experiment: N2 vs N2 mixed stage for control RNA
Red RNA:
Green RNA:
Experimental details:
Growth conditions:
Comments:
Contact name:CBV

Coded name:Exp11
Experiment number:1
Chip version:Rosetta #11425 (2nd printing)
Description of experiment: GL133(rf10) vs. GL133(rf10) heat shock
Red RNA:GL133(rf10) heat shock
Green RNA:GL133(rf10)
Experimental details:
Growth conditions:
Comments:
Contact name:Gordon Lithgow/David Walker

Coded name:Exp12
Experiment number:1
Chip version:Rosetta #11426 (2nd printing)
Description of experiment: GL112(rf17) vs GL112(rf17) heat shock
Red RNA:GL112(rf17) heat shock
Green RNA:GL112(rf17)
Experimental details:
Growth conditions:
Comments:
Contact name:Gordon Lithgow/David Walker

Coded name:Series1
Experiment number:1
Chip version:Rosetta #11422, 11423, 11424, 11427, 11428, 11429, 11430 (2nd printing)
Description of experiment:N2 #2 timecourse timepoints vs vjr N2 mixed control RNA
Red RNA:vjr N2 mixed control RNA
Green RNA:timepoints T0-T6
Experimental details:Timepoints were harvested from staged L3 worms beginning at approx. 32 hr after hatched L1's were fed and plated.
Growth conditions:
Comments:T1 was repeated a second time
Contact name:CBV

Coded name:Exp13
Experiment number:1
Chip version:Rosetta #10947
Description of experiment:vjr N2 mixed stage prep1 vs vjr N2 mixed stage prep 2
Red RNA: N2 mixed stage prep 2
Green RNA: N2 mixed stage prep1
Experimental details:
Growth conditions:
Comments:
Contact name:vjr

Coded name:Exp14
Experiment number:1, 2
Chip version:Rosetta #11434, #11437
Description of experiment:smg-1 vs N2
Red RNA:N2
Green RNA:smg-1
Experimental details:
Growth conditions:
Comments:
Contact name: Andrew Grimson

Coded name:Exp15
Experiment number:1
Chip version:Rosetta #10982
Description of experiment: N2-1T4 vs vjr N2 mixed control
Red RNA:vjr N2 mixed control
Green RNA:N2-1T4
Experimental details:
Growth conditions:
Comments:
Contact name:vjr

Coded name:Exp23
Experiment number:1,2
Chip version:Rosetta #11436, 11438
Description of experiment:smg-5 vs N2
Red RNA:N2
Green RNA:smg-5
Experimental details:
Growth conditions:
Comments:
Contact name:Andrew Grimson

Coded name:Exp34
Experiment number:1,2
Chip version:Rosetta #11446, 11447
Description of experiment:N2 young adult vs N2 (C,D) and (G,H) heat shock
Red RNA:N2 heat shock
Green RNA:N2 young adult
Experimental details:
Growth conditions:
Comments:
Contact name:Gordon Lithgow

Coded name:Exp35
Experiment number:1
Chip version:Rosetta #11449
Description of experiment:glp-1 0hr vs wt0hr
Red RNA:wt 0hr
Green RNA: glp-1 0hr
Experimental details:
Growth conditions:
Comments:
Contact name:Judith Kimble

Coded name:Exp36
Experiment number:1,2
Chip version:Rosetta # 11450, 11454
Description of experiment:dvIs2 vs dvIs2 dv56
Red RNA:dvIs2 dv56
Green RNA:dvIs2
Experimental details:
Growth conditions:
Comments:
Contact name:Chris Link

Coded name:Series2
Experiment number:2
Chip version:Rosetta #11452, 11453, 11458, 11459, 11462, 11465, 11466
Description of experiment:N2 timecourse #3 T0, T1, T2, T3, T4, T5, T6 vs. vjr N2 control
Red RNA:vjr N2 control
Green RNA:N2 #3 T0, T1, T2, T3, T4, T5, T6
Experimental details:
Growth conditions:
Comments:10 ug poly A+ RNA used for timepoints T0-T3, 5 ug for control
Contact name:CBV

Coded name:Exp37
Experiment number:1
Chip version:Rosetta #11455
Description of experiment:glp-1 1.5 hr vs wt 1.5 hr
Red RNA:wt 1.5hr
Green RNA: glp-1 1.5hr
Experimental details:
Growth conditions:
Comments:
Contact name:Judith Kimble

Coded name:Exp38
Experiment number:1
Chip version:Rosetta #11456
Description of experiment:glp-1 3hr vs wt 3hr
Red RNA:wt 3hr
Green RNA: glp-1 3hr
Experimental details:
Growth conditions:
Comments:
Contact name:Judith Kimble

Coded name:Exp39
Experiment number:1
Chip version:Rosetta #11457
Description of experiment:glp-1 4hr vs wt 4hr
Red RNA:wt 4hr
Green RNA: glp-1 4hr
Experimental details:
Growth conditions:
Comments:
Contact name:Judith Kimble

Coded name: Exp54
Experiment number:1,2
Chip version: Rosetta # 11460, 11461, 11477
Description of experiment:lin-14 (n179ts) vs N2
Red RNA:N2
Green RNA:lin-14 (n179ts)
Experimental details:
Growth conditions:
Comments:
Contact name:Ambrose Lab, Marta Hristova

Coded name:Series 3
Experiment number:1st timecourse prep
Chip version:11467, 11468, 11469, 11470, 11475, 11480. 11481
Description of experiment:let-23(sy1) T0, T1, T2, T3, T4,T5, T6 vs. vjr N2 control
Red RNA:vjr N2 control
Green RNA:let-23(sy1) T0-T6
Experimental details:
Growth conditions:
Comments:
Contact name:CBV

Coded name:Series 4
Experiment number:2nd timecourse prep
Chip version:11471, 11476
Description of experiment:let-23(sy1) T5, T6 vs vjr control
Red RNA:vjr N2 control
Green RNA:let-23(sy1) T5, T6
Experimental details:
Growth conditions:
Comments:
Contact name:

Coded name:Series 5
Experiment number:1st timecourse prep
Chip version:11472, 11474, 11483, 11484, 11485
Description of experiment:let-60(n1046) T0, T1, T2, T5, T6 vs vjr N2 control
Red RNA:vjr N2 control
Green RNA:let-60(n1046) T0, T1, T2, T5, T6
Experimental details:
Growth conditions:
Comments:
Contact name:CBV

Coded name:Series 6
Experiment number:2nd timecourse prep
Chip version:11473
Description of experiment:let-60(n1046) T5 vs vjr control
Red RNA:vjr control
Green RNA:let-60(n1046) T5
Experimental details:
Growth conditions:
Comments:
Contact name:CBV

Coded name:Exp55
Experiment number:1
Chip version:Rosetta #11478
Description of experiment:N2 shocked vs N2 unshocked
Red RNA:N2 unshocked
Green RNA:N2 shocked
Experimental details:used 8 ug RNA each
Growth conditions:staged gravid 3-4 day adults at 20C
Comments:heat shock 1hr at 35C
Contact name:Pat Tedesco

Coded name:Exp56
Experiment number:1
Chip version:11479
Description of experiment:age-1(hx546) shocked vs age-1(hx546) unshocked
Red RNA:age-1(hx546) unshocked
Green RNA:age-1(hx546) shocked
Experimental details:used 8 ug each of RNA for labelling
Growth conditions:staged gravid 3-4 day adults at 20C
Comments:heat shock 1 hr at 35C
Contact name:Pat Tedesco

Coded name:Exp57
Experiment number:1,2,3
Chip version:Rosetta #11486, #11490, #11491
Description of experiment:unstaged N2 (A1, A2, A3) vs unstaged ace-1;ace-2 (B1, B2, B3)
Red RNA:unstaged N2 (A1, A2, A3)
Green RNA:unstaged ace-1;ace-2 (B1, B2, B3)
Experimental details:
Growth conditions:
Comments:
Contact name:Schafer lab, Stanley Shyn

Coded name:Exp58
Experiment number:#11487
Chip version:1
Description of experiment:age-1(hx546) shocked vs N2 shocked
Red RNA:N2 shocked
Green RNA:age-1(hx546) shocked
Experimental details:
Growth conditions:
Comments:
Contact name:Pat Tedesco

Coded name:Exp59
Experiment number:1
Chip version:#11488
Description of experiment:age-1(hx546) unshocked vs N2 unshocked
Red RNA:N2 unshocked
Green RNA:age-1(hx546) unshocked
Experimental details:
Growth conditions:
Comments:Pat Tedesco
Contact name:

Coded name:Exp 67
Experiment number:1
Chip version:Rosetta #11518
Description of experiment:nicotine treated staged N2 vs no drug staged N2
Red RNA: staged N2, no drug
Green RNA:nicotine treated staged N2
Experimental details:
Growth conditions:
Comments:
Contact name:Shafer lab

Coded name: Exp68
Experiment number:1
Chip version:Rosetta # 11541
Description of experiment:tam-1(cc567) vs myo-3::gfp control
Red RNA:myo-3::gfp control
Green RNA:tam-1(cc567)
Experimental details:
Growth conditions:
Comments:
Contact name:Andy Fire Lab, Jenny Hsieh

Coded name:Exp69
Experiment number:1, 2
Chip version:Rosetta #11520, 11519
Description of experiment:mec-3 gain of function vs mec-3 loss of function
Red RNA:mec-3 lf (lf2 U6 and lf1 U6)
Green RNA:mec-3 gf (gf2 TU2387 and gf1TU2387)
Experimental details:
Growth conditions:
Comments:
Contact name:Yun, Chalfie Lab

Coded name:
Experiment number:1
Chip version:
Description of experiment:
Red RNA:
Green RNA:
Experimental details:
Growth conditions:
Comments:
Contact name: