Editing
Kun:LabNotes/SingleCellExpr/2011-9-7
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
===Looking for differentially expressed genes=== *I just realized that when feeding cuffdiff with a gtf file generated by cuffcompare, all the gene names are XLOC_xxxxx, which are difficult to link to the known genes. So I changed the gtf file to the UCSC mouse genes.gtf. /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 8 -o cuffDiff_E9.5_vs_E11.5 tophat_Mm_Indx3/accepted_hits.bam,tophat_Mm_Indx7/accepted_hits.bam tophat_Mm_Indx4/accepted_hits.bam,tophat_Mm_Indx8/accepted_hits.bam /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 8 -o cuffDiff_E11.5_vs_wtE13.5f tophat_Mm_Indx4/accepted_hits.bam,tophat_Mm_Indx8/accepted_hits.bam tophat_Mm_Indx6/accepted_hits.bam,tophat_Mm_Indx11/accepted_hits.bam,tophat_Mm_Indx12/accepted_hits.bam /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 8 -o cuffDiff_E11.5_vs_wtE13.5m tophat_Mm_Indx4/accepted_hits.bam,tophat_Mm_Indx8/accepted_hits.bam tophat_Mm_Indx5/accepted_hits.bam,tophat_Mm_Indx9/accepted_hits.bam,tophat_Mm_Indx10/accepted_hits.bam /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 8 -o cuffDiff_wtE13.5m_vs_wtE13.5f tophat_Mm_Indx5/accepted_hits.bam,tophat_Mm_Indx9/accepted_hits.bam,tophat_Mm_Indx10/accepted_hits.bam tophat_Mm_Indx6/accepted_hits.bam,tophat_Mm_Indx11/accepted_hits.bam,tophat_Mm_Indx12/accepted_hits.bam /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf -N -p 8 -o cuffDiff_wtE13.5f_vs_koE13.5f tophat_Mm_Indx6/accepted_hits.bam,tophat_Mm_Indx11/accepted_hits.bam,tophat_Mm_Indx12/accepted_hits.bam tophat_Mm_Indx14/accepted_hits.bam,tophat_Mm_Indx15/accepted_hits.bam Wild-type: E9.5 vs. E11.5 Wild-type: E11.5 vs. E13.5-female [[Image:FPKM_wtE9.5_vs_wtE11.5.png|300px]][[Image:FPKM_wtE11.5_vs_wtE13.5f.png|300px]] [[Media:FPKM_wtE9.5_vs_wtE11.5.xlsx|Data]] [[Media:FPKM_wtE11.5_vs_wtE13.5f.png.xlsx|Data]] Wild-type: E113.5-male vs. E13.5-female E13.5-female: wild-type vs. TET1-KO [[Image:FPKM_wtE13.5m_vs_wtE13.5f.png|300px]][[Image:FPKM_wtE13.5f_vs_koE13.5f.png|300px]] [[Media:FPKM_wtE13.5m_vs_wtE13.5f.xlsx|Data]] [[Media:FPKM_wtE13.5f_vs_koE13.5f.png.xlsx|Data]] *I randomly picked a few genes that showed biggest differences, and checked their functions. Clearly the data make sense biologically. Examples include: **Dazl and Sohlh2 were up-regulated by over 100-fold from E9.5 to E11.5. **Taf7l was up-regulated by ~50 folds from E11.5 to E13.5f. **Lefty1 and Lefty2 expressed at >100x higher in E13.5m than in E13.5f. **Tet1's expression was almost completely lost in ko-E13.5f.
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information