SAGE Library SM151

Classification

Library Name SM151
Species Mus musculus
Strain C57BL/6J
Mutation Wild Type
Location Small intestine - Epithelium
Sex Unknown
Age E12
Developmental Stage Theiler Stage 20
Organsim Condition

Sample Collection

Tissue Dissection Photos

Click to view full-size image…

With the aid of a dissecting microscope the small intestine was manually dissected from embryos submerged in phosphate buffered saline (PBS). The isolation of epithelium is 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 addition 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. Epithelial tissue was teased away from mesenchyme tissue with either tungsten needles or fine forceps. Epithelial tissue was then collected into Trizol. Epithelium 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

SM151 has been merged with technical replicate library SM159.

Merged Library Name SM151_SM159
Total Raw Tags (no quality cut-off) 101,430
Total Raw Tags at Q95 77,401
Total Raw Tags at Q99 75,049
Unique Tags 26,734

Data

Tag Counts at Quality 0.95 cut-off tagcounts-750_SM151_SM159_Q95.txt
Tag Counts at Quality 0.99 cut-off tagcounts-750_SM151_SM159_Q99.txt
Clustered Tag Counts and P-Value tagclustered-750_SM151_SM159.txt
Original Tag Set
Total Raw Tags (no quality cut-off) 49,914
Total Raw Tags at Q95 42,054
Total Raw Tags at Q99 40,316
Unique Tags 16,556

Data

Library Metadata Library Metadata XML
Tag Counts at Quality 0.95 cut-off tagcounts_SM151_Q95.txt
Tag Counts at Quality 0.99 cut-off tagcounts_SM151_Q99.txt
Clustered Tag Counts and P-Value tagclustered_SM151.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.

SAGE Library Help

A full explanation of each of the fields displayed on this page is available on the SAGE Library Help page.