SAGE Library SM095

Classification

Library Name SM095
Species Mus musculus
Strain C57BL/6J
Mutation Wild Type
Location Small intestine - Mesenchyme
Sex Unknown
Age E12
Developmental Stage Theiler Stage 20
Organsim Condition

Sample Collection

Tissue Dissection Photos

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With the aid of a dissecting microscope the small intestine was manually dissected from embryos submerged in in phosphate buffere saline (PBS). The isolation of mesenchyme was performed as described by Nagy et al (2003). The small 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. 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: Pamela Hoodless Lab
Number of Animals 53

Library Construction

SAGE Protocol SAGE (LongSAGE 21 bp)
Starting RNA 5.0 ug

Tag Extraction

Total Raw Tags (no quality cut-off) 105,374
Total Raw Tags at Q95 95,041
Total Raw Tags at Q99 91,722
Unique Tags 25,854

Data

Library Metadata Library Metadata XML
Tag Counts at Quality 0.95 cut-off tagcounts_SM095_Q95.txt
Tag Counts at Quality 0.99 cut-off tagcounts_SM095_Q99.txt
Clustered Tag Counts and P-Value tagclustered_SM095_Q99.txt

Data Analysis

DiscoverySpace

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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