SAGE Library SM078


Library Name SM078
Species Mus musculus
Strain C57BL/6J
Mutation Wild Type
Location Large intestine - Mesenchyme
Sex Unknown
Age E12.5
Developmental Stage Theiler Stage 20
Organsim Condition

Sample Collection

Tissue Dissection Photos

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With the aid of a dissecting microscope the large intestine was manually dissected from embryos submerged in in phosphate buffere saline (PBS). The isolation of mesenchyme is as described by Nagy et al (2003). The large intestines were then transferred to a Petri dish containing 200 ul of 1% trypsin in Hanks solution. The trypsin was allowed to act on the tissue for 20 minutes at room temperature. The digestion process was stopped with the addtion of ~1 ml of 20% fetal bovine serum (FBS) in Hanks solution plus a small amount of DNAse powder. The caecum was removed and not included in the tissue collection. Mesenchymal tissue was teased away from epithelial tissue with either tungsten needles or fine forceps. Mesenchymal tissue was then collected into Trizol. Mesenchyme from embryos of several litters was collected to obtain enough RNA for SAGE library construction.

Creative Commons License
This work is licensed under a Creative Commons Attribution 2.5 License.
Lab BCCRC: Cheryl Helgason Lab
Number of Animals 66

Library Construction

SAGE Protocol SAGE (LongSAGE 21 bp)
Starting RNA 10.0 ug

Tag Extraction

Total Raw Tags (no quality cut-off) 105,132
Total Raw Tags at Q95 86,078
Total Raw Tags at Q99 80,251
Unique Tags 31,211


Library Metadata Library Metadata XML
Tag Counts at Quality 0.95 cut-off tagcounts_SM078_Q95.txt
Tag Counts at Quality 0.99 cut-off tagcounts_SM078_Q99.txt
Clustered Tag Counts and P-Value tagclustered_SM078_Q99.txt

Data Analysis


Data is available for analysis using DiscoverySpace, a cross-platform application that allows comparison between SAGE libraries, tag to gene mapping and results from public datasources.

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