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Summary
RNA-seq on ventral midbrains, all animals ~ 3 months old.
Collaborative Cross: 1 male per strain for 32 CC strains.
C57BL/6J, A/J, and DBA/2J: The value is the mean of 12 samples (6 males + 6 females).
Experiment design
Single-end 75bp reads at a depth of about 30 million reads/sample. Processed by Yujuan Gui using both RPKM and TPM. Log2 of TPM+1 uploaded into GeneNetwork Dec 2019 by Arthur Centeno and Robert W. Williams.
Half of the C57BL/6J and A/J were sequenced in Genomics Core Facility - EMBL Heidelberg with single-end 80bp reads at a depth of about 30 million reads/sample.
About cases
CC mice were bred by Dr. Klaus Schughart at the HZI, Braunschweig, Germany.
Note: Only one of 8 - 10 male samples was processed for RNA-seq (unilateral dissection of VMB). Luxembourg team also has 8 - 10 female samples. 16 to 20 complete brain hemispheres fixed in paraformaldehyde for 48 hours and then transferred to PBS with sodium azide (now stored at 4 degree Celsius at BT1, 7 ave des Hauts-Fourneaux, L-4362 Esch-sur-Alzette).
C57BL/6J, A/J, and DBA/2J were bred by University of Luxembourg.
About tissue
Ventral midbrains
About platform
Illumina NextSeq 5000
About data processing
Sequencing data processed by Yujuan Gui. Sequencing data were TPM transformed then log2.
Contributors
Team of Investigators:
Lasse Sinkkkonen (lasse.sinkkonen@uni.lu), Manuel Buttini (manuel.buttini@uni.lu), Yujuan Gui (yujuan.gui@uni.lu), and Melanie Thomas at the University of Luxembourg
Data entered into GeneNetwork December 2019 by Arthur G. Centeno, Robert W. Williams, Yujuan Gui
Acknowledgment
LS and MB would like to thank the Luxembourg National Research Fund (FNR) for the support (FNR CORE C15/BM/10406131 grant).
Notes
Important links:
Compgen tool suite CC mice.
COLLABORATIVE CROSS AND DIVERSITY OUTBRED REFERENCE DATA.