User contributions for Marina
From FANTOM5_SSTAR
19 February 2015
- 11:1111:11, 19 February 2015 diff hist +60 Protocols:rRNAdust No edit summary current
16 February 2015
- 10:1810:18, 16 February 2015 diff hist +324 Protocols:HeliScopeCAGE read alignment No edit summary current
5 September 2012
- 18:2418:24, 5 September 2012 diff hist +55 Protocols:HeliScopeCAGE read alignment No edit summary
- 18:2318:23, 5 September 2012 diff hist 0 N File:Delve User Manual.pdf No edit summary current
- 18:2118:21, 5 September 2012 diff hist +1,214 Protocols:HeliScopeCAGE read alignment No edit summary
3 September 2012
- 16:3016:30, 3 September 2012 diff hist +12 Protocols:RNAseq No edit summary current
- 16:2916:29, 3 September 2012 diff hist 0 N File:Note2 309pl1210.pdf No edit summary current
- 16:2916:29, 3 September 2012 diff hist 0 N File:Note1 2008729133616244.pdf No edit summary current
- 16:2916:29, 3 September 2012 diff hist +3,599 N Protocols:RNAseq Created page with "Sequencing libraries was constructed starting from 2 μg of total RNA. rRNA removal step is executed by (Dynabeads Oligo(dT)25 treatment or Ribo-Zero treatment) [1]. If rRNA r..."
- 13:5513:55, 3 September 2012 diff hist +1 Protocols →Computational analysis current
- 13:5413:54, 3 September 2012 diff hist −20 Protocols →Computational analysis
- 13:5313:53, 3 September 2012 diff hist −43 OP-HELISCOPE-sequencing-v1.0 No edit summary current
- 13:5213:52, 3 September 2012 diff hist −113 OP-HELISCOPE-sequencing-v1.0 No edit summary
- 13:5013:50, 3 September 2012 diff hist 0 N File:LB-017 01, Low-Volume Sample Loading Protocol.pdf No edit summary current
- 13:5013:50, 3 September 2012 diff hist 0 N File:LB-016 01, Sample Loader Manual.pdf No edit summary current
- 13:4913:49, 3 September 2012 diff hist 0 N File:Helicos ChIP Seq Protocol.pdf No edit summary current
- 13:4313:43, 3 September 2012 diff hist +8 OP-HiSeq2000-sequencing-cBot-v3.0 No edit summary current
- 13:4213:42, 3 September 2012 diff hist +8 OP-HiSeq2000-sequencing-cBot-v2.5 No edit summary current
- 13:4113:41, 3 September 2012 diff hist +4 OP-SOLEXA-shortRNA-TruSeq-v2.0 No edit summary current
- 13:3813:38, 3 September 2012 diff hist 0 N File:TruSeq SmallRNA SamplePrep Guide 15004197 C.pdf No edit summary current
- 13:3813:38, 3 September 2012 diff hist 0 N File:HiSeq2000 UserGuide 15011190 D.pdf No edit summary current
- 13:3713:37, 3 September 2012 diff hist 0 N File:CBot UserGuide 15006165 F.PDF No edit summary current
- 13:3713:37, 3 September 2012 diff hist 0 N File:CBot UserGuide 15006165 C.pdf No edit summary current
- 13:3613:36, 3 September 2012 diff hist 0 N File:Cms 059303.pdf No edit summary current
- 13:3513:35, 3 September 2012 diff hist +28 Protocols:RNA extraction No edit summary current
- 13:3313:33, 3 September 2012 diff hist +1 Protocols:RNA extraction No edit summary
- 13:3113:31, 3 September 2012 diff hist 0 N File:RNeasy MinElute Cleanup Handbook.pdf No edit summary current
- 13:3113:31, 3 September 2012 diff hist +121 Protocols:RNA extraction No edit summary
- 13:2413:24, 3 September 2012 diff hist 0 N File:Trizol isopropanol ver1.pdf No edit summary current
- 13:2413:24, 3 September 2012 diff hist 0 N File:Trizol ethanol ver1.pdf No edit summary current
- 13:2313:23, 3 September 2012 diff hist 0 N File:Totally RNA ver1.pdf No edit summary current
- 13:0013:00, 3 September 2012 diff hist +17 Protocols:RNA extraction No edit summary
- 12:5412:54, 3 September 2012 diff hist 0 N File:MiRNEasy ver1.pdf No edit summary current
- 11:4711:47, 3 September 2012 diff hist +133 Protocols:SmallRNAseq No edit summary current
- 11:3811:38, 3 September 2012 diff hist −1 Protocols →Computational analysis
- 11:3811:38, 3 September 2012 diff hist −4 Protocols →Computational analysis
- 11:3811:38, 3 September 2012 diff hist +235 Protocols →Computational analysis
- 11:3211:32, 3 September 2012 diff hist +3,341 N OP-HiSeq2000-sequencing-cBot-v3.0 Created page with "Step 1. Prepare Sample DNA for Cluster Generation Combine the template DNA [template_DNA_concentration][1] nM and 0.1 N NaOH. Vortex briefly to mix the template solution. Cen..."
- 11:3011:30, 3 September 2012 diff hist +38 Protocols:SmallRNAseq No edit summary
- 11:1511:15, 3 September 2012 diff hist +2 OP-SOLEXA-shortRNA-TruSeq-v2.0 No edit summary
- 11:1411:14, 3 September 2012 diff hist +1,832 N OP-SOLEXA-shortRNA-TruSeq-v2.0 Created page with "Library constructed with manufacture's protocol [1] with using 'TruSeq Small RNA Sample Prep Kit' (Catalog #: RS-200-0012, RS-200-0024, RS-200-0036, RS-200-0048). This protoco..."
- 11:1111:11, 3 September 2012 diff hist +2,790 N OP-HiSeq2000-sequencing-cBot-v2.5 Created page with "Step 1. Prepare Sample DNA for Cluster Generation Denature the template DNA with 2 N NaOH to a final DNA concentration [1] and final NaOH concentration of 0.1 N [2]. Incubate..."
- 11:0911:09, 3 September 2012 diff hist +80 N Protocols:SmallRNAseq Created page with "* OP-SOLEXA-shortRNA-TruSeq-v2.0 * OP-HiSeq2000-sequencing-cBot-v2.5 * *"
- 10:5110:51, 3 September 2012 diff hist +52 Protocols:RNA extraction No edit summary
31 August 2012
- 13:5913:59, 31 August 2012 diff hist −135 Protocols:Motif Activity Response Analysis(MARA) No edit summary current
- 13:5813:58, 31 August 2012 diff hist −3,472 Protocols:Motif Activity Response Analysis(MARA) No edit summary
- 13:4813:48, 31 August 2012 diff hist +7,506 N Protocols:Motif Activity Response Analysis(MARA) Created page with "Calculating motif activities in 7 easy steps ============================================ Last updated: 2012.03.29 OSC Table input file requirements -----------------------..."
- 13:0313:03, 31 August 2012 diff hist +3,162 N OP-Illumina-sequencing-PairedEnd-v3.0 Created page with "Protocol: OP-SOLEXA-sequencing-PairedEnd-v3.0 Author: Kaida, Kaoru Created: Sep 17th, 2010 Update: Jul 6th, 2011 Parameters: machine, run, lane, DNA_concentrations, softw..." current
- 13:0213:02, 31 August 2012 diff hist +4,121 N OP-SOLEXA-nanoCAGE-Direct-v1.4 Created page with "Protocol: OP-SOLEXA-nanoCAGE-Direct-v1.4-step1 Author: Salimullah, Md. Created: September 2, 2009 Update: July 8, 2010 Parameters: RNA-mass, RNA-volume, reverse-transcrip..." current
- 13:0213:02, 31 August 2012 diff hist +8 Protocols:nanoCAGEscan No edit summary current
- 11:0911:09, 31 August 2012 diff hist +2,695 N OP-HELICOS-CAGE-Filtering-v1.0 Created page with "Protocol: OP-HELICOS-CAGE-Filtering-v1.0 Author: Katayama, Shintaro Created: July 8, 2010 Updated: July 16, 2010 Parameters: Description: FilterSMS in helisphere-0.14.a..." current
- 11:0811:08, 31 August 2012 diff hist +1,807 N OP-HELISCOPE-sequencing-v1.0 Created page with "Protocol: OP-HELISCOPE-sequencing-v1.0 Author: Kawashima, Tsugumi Created: Apr 11th, 2011 Update: Apr 11th, 2011 Parameters: machine, run, flowcell, channel Description:..."
- 11:0611:06, 31 August 2012 diff hist +6,403 N OP-HELISCOPE-CAGE-v4.0 Created page with "Protocol: OP-HELISCOPE-CAGE-v4.0 Author: Kojima, Miki Created: Apr. 28, 2011 Update: Parameters: Description: Sample preparation unit is 96 wells. Sample is prepared b..." current
- 11:0511:05, 31 August 2012 diff hist +5,338 N OP-HELISCOPE-CAGE-v5.0 Created page with "Protocol: OP-HELISCOPE-CAGE-v5.0 Author: Kojima, Miki Created: Nov. 25, 2010 Update: Parameters: Description: Start total RNA amount is under 1. µg Sample preparation..." current
- 11:0511:05, 31 August 2012 diff hist +12 Protocols:Low quantity HeliScopeCAGE No edit summary current
- 11:0311:03, 31 August 2012 diff hist +5,201 N OP-HELISCOPE-CAGE-v3.12 Created page with "Protocol: OP-HELISCOPE-CAGE-v3.12 Author: Kojima, Miki Created: Nov. 25, 2010 Update: Parameters: Description: Sample preparation unit is 8 strips. Reagent and sample ..." current
- 11:0311:03, 31 August 2012 diff hist +16 Protocols:HeliScopeCAGE No edit summary current
- 11:0011:00, 31 August 2012 diff hist +156 Protocols:RNA extraction No edit summary
- 10:4910:49, 31 August 2012 diff hist −4 Protocols:RNA extraction No edit summary
- 10:4810:48, 31 August 2012 diff hist +862 N OP-RNA-extraction-totalRNA-RiboPure minelute cleanup-v1.0 Created page with "Protocol: OP-RNA-extraction-totalRNA-RiboPure_minelute_cleanup-v1.0 Protocol name: Ribopure Blood RNA extraction and RNeasy MinElute Cleanup protocol Version: v1.0 Author: Amb..." current
- 10:4710:47, 31 August 2012 diff hist +4 Protocols:RNA extraction No edit summary
30 August 2012
- 16:3216:32, 30 August 2012 diff hist −1,433 Protocols:HeliScopeCAGE No edit summary
- 15:5315:53, 30 August 2012 diff hist +52 Protocols:nanoCAGEscan No edit summary
- 15:5115:51, 30 August 2012 diff hist −64 Protocols:HeliScopeCAGE →Known facts about HeliScope technology
- 14:5014:50, 30 August 2012 diff hist +1,497 Protocols:HeliScopeCAGE No edit summary
- 14:4014:40, 30 August 2012 diff hist +29 Protocols:HeliScopeCAGE read alignment No edit summary
- 12:0812:08, 30 August 2012 diff hist +394 N Protocols:nanoCAGEscan Created page with "CAGEscan libraries are prepared using the nanoCAGE protocol, version 1.4 (OP-SOLEXA-nanoCAGE-Direct-v1.4), and sequenced paired-end according to standard procedures on Illumin..."
- 12:0712:07, 30 August 2012 diff hist +610 N Protocols:HeliScopeCAGE read alignment Created page with "The data sequenced on Heliscope sequencers are post processed, in order to: *Discard the CAGE tags derived from the ribosomal DNA repeating unit, which is not contained in ..."
- 12:0412:04, 30 August 2012 diff hist +434 N Protocols:Low quantity HeliScopeCAGE Created page with "We started HeliScope CAGE with manual operation (with multi(8)-channel pipet), and achieved also automated preparation of the CAGE libraries to scale up the number of profiles..."
- 12:0412:04, 30 August 2012 diff hist −67 Protocols:HeliScopeCAGE No edit summary
- 12:0212:02, 30 August 2012 diff hist +553 N Protocols:HeliScopeCAGE Created page with "We started HeliScope CAGE with manual operation (with multi(8)-channel pipet), and achieved also automated preparation of the CAGE libraries to scale up the number of profiles..."
- 11:5511:55, 30 August 2012 diff hist +498 N Protocols:rRNAdust Created page with "This step is required to remove reads corresponding to rRNA from Helicos CAGE datasets. Since the error rate of Helicos is high and includes many insertion / deletion errors..."
- 11:3711:37, 30 August 2012 diff hist +315 N Protocols:RNA extraction Created page with "We have used various RNA extraction protocols in FANTOM project. *OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0 *OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0 *OP-RNA-ex..."
