Lizio 2017, Transcription profiling in rat tissues.

Description

TSS mapping done with CAGE of rat (Rattus norvegicus) aortic smooth muscle cell, hepatocyte and mesenchymal stem cells.

Source

Samples

From R. norvegicus (Jul 2014 Rnor_6.0/rn6).

Transcription Profiling data:

Filename Description Feature GEO-ID
1 RatAorticSmoothMuscleCells-Differentiated_cDonor1.CNhs12070.11481-119D5.rn6.nobarcode.sga Aortic Smooth Muscle cells|differentiated|donor1 CAGE -
2 RatAorticSmoothMuscleCells-Differentiated_cDonor2.CNhs12071.11482-119D6.rn6.nobarcode.sga Aortic Smooth Muscle cells|differentiated|donor2 CAGE -
3 RatAorticSmoothMuscleCells-Differentiated_cDonor3.CNhs12072.11483-119D7.rn6.nobarcode.sga Aortic Smooth Muscle cells|differentiated|donor3 CAGE -
4 RatAorticSmoothMuscleCells_cDonor1.CNhs11298.11300-117B4.rn6.nobarcode.sga Aortic Smooth Muscle cells|donor1 CAGE -
5 RatAorticSmoothMuscleCells_cDonor2.CNhs11307.11377-118A9.rn6.nobarcode.sga Aortic Smooth Muscle cells|donor2 CAGE -
6 RatAorticSmoothMuscleCells_cDonor3.CNhs11315.11449-118I9.rn6.nobarcode.sga Aortic Smooth Muscle cells|donor3 CAGE -
7 RatMesenchymalStemCells-BoneMarrowDerived_cDonor1.CNhs11295.11296-117A9.rn6.nobarcode.sga Mesenchymal stem cells|bone marrow derived|donor1 CAGE -
8 RatMesenchymalStemCells-BoneMarrowDerived_cDonor2.CNhs11301.11373-118A5.rn6.nobarcode.sga Mesenchymal stem cells|bone marrow derived|donor2 CAGE -
9 RatMesenchymalStemCells-BoneMarrowDerived_cDonor3.CNhs11313.11445-118I5.rn6.nobarcode.sga Mesenchymal stem cells|bone marrow derived|donor3 CAGE -
10 RatHepatocytes_cDonor1.CNhs11293.11295-117A8.rn6.nobarcode.sga hepatocytes|donor1 CAGE -
11 RatHepatocytes_cDonor2.CNhs11302.11372-118A4.rn6.nobarcode.sga hepatocytes|donor2 CAGE -
12 RatHepatocytes_cDonor3.CNhs11312.11444-118I4.rn6.nobarcode.sga hepatocytes|donor3 CAGE -
13 UniversalRNA-RatNormalTissuesBiochain_cPool1.CNhs10614.10009-101B8.rn6.nobarcode.sga Universal RNA|Normal Tissues Biochain|pool1 CAGE -

Technical Notes

BAM files werw converted to BED using bamToBed v2.12.0 (bedtools) and to SGA using bed2sga.pl (ChIP-Seq v. 1.5.3).

References

Last update: 1 Oct 2018