Data Set Group2: UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM

Data Set: UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed GN Accession: GN164 GEO Series: Title: Organism: Mouse (Mus musculus, mm10) Group: BXD Tissue: Brain mRNA Dataset Status: Public Platforms: ABI SOLiD Normalization: RPKM

Contact Information Robert Williams University of Tennessee Health Science Center 71 S Manassas St, Room 405 TSRB Memphis, TN 38163 USA Tel. 901 448-7050 rwilliams@uthsc.edu Website Download datasets and supplementary data files GN164_MeanDataAnnotated_rev081815.txt (N/A) GN164_StdError_rev081815.txt (N/A)

Specifics of this Data Set:

Note: March 2019: now actually 449 transcripts/genes with LRS > 23 and peak LRS is still 102.6.

Summary:

UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Trimmed dataset have been re-normalized by forcing values down to zero at level of individual mRNA seq assay.

About the cases used to generate this set of data:

Index Original Strain Corrected Strain Sex Age 1 BXD13_batch2 BXD18 M 67 2 BXD15_batch2 BXD15 F 62 3 BXD18_batch2 BXD19 F 65 4 BXD24_batch2 BXD24 F 63 5 BXD36_batch2 BXD45 removed M 67 6 BXD39_batch2 BXD39 F 60 7 BXD42_batch2 BXD43 F 67 8 BXD43_batch2 BXD42 F 60 9 BXD45_batch2 BXD45 F 60 10 BXD50_batch2 BXD50 F 57 11 BXD51_batch2 BXD55 F 59 12 BXD55_batch2 BXD51 F 61 13 BXD56_batch2 BXD56 F 67 14 BXD6_batch2 BXD6 F 59 15 BXD8_batch2 BXD9 F 62 16 BXD9_batch2 BXD8 M 70 17 BXD14_batch3 BXD40 F 76 18 BXD16_batch3 BXD19 M 74 19 BXD32_batch3 BXD32 M 54 20 BXD38_batch3 BXD38 F 102 21 BXD40_batch3 BXD14 M 81 22 BXD48_batch3 BXD48 M 68 23 BXD60_batch3 BXD60 F 64 24 BXD66_batch3 BXD66 M 61 25 BXD69_batch3 BXD69 F 66 26 BXD70_batch3 BXD70 M 72 27 BXD29m_batch4 BXD1 F 60 28 BXD29n_batch4 BXD29 F 344 29 BXD34_batch4 BXD34 F 108 30 BXD49_batch4 BXD49 M 76 31 BXD65_batch4 BXD29 F 58 32 BXD22_batch6 BXD22 F 67

About the tissue used to generate this set of data:

About the array platform:

About data values and data processing:

Notes:

RNA sequencing for BXD strains on SOLiD by David Li. All Bam files alignment done by Xusheng Wang Aligned files were uploaded to Partek Genomic Suite 6.5 (version 6.10.0810) and processed by K Mozhui Normalization: RPKM (reads per kilobase per million mapped reads) Batch effect due to low exonic reads for batch 2 Revision 1.6 Untrimmed (current) LRS=(23 999) ->350 records Max LRS = 102.6 Record Id:uthsc_nr_015498, Gene Symbol:1500004A13Rik **Note: 1 sample BXD45 and BXD34 removed. BXD41 switched to BXD1 as a second posible candidate. Revision 1.5 Untrimmed LRS=(23 999) ->268 records Max LRS = 80.0 Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1 **Note: 1 sample BXD45 removed. BXD41 switched to BXD1 as a second posible candidate. Revision 1.4 Untrimmed LRS=(23 999) ->246 records Max LRS = 80.0 Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1 **Note: 1 sample BXD45 removed and keep BXD41 Revision 1.3 Untrimmed LRS=(23 999) ->233 records Max LRS = 80.7 Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1 Revision 1.2 Untrimmed LRS=(23 999) ->190 records Max LRS = 56.9 Record Id:uthsc_nr_003513, Gene Symbol:Neat1 Revision 1 Untrimmed LRS=(23 999) ->126 records Max LRS = 35.3 Record Id:uthsc_nm_001113412, Gene Symbol:Fggy

Experiment Type:

Contributor:

Citation:

Data source acknowledgment:

Study Id:

157

• The UT Center for Integrative and Translational Genomics
• NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
• NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
• NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
• NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)