SAGE Library SM155

Classification

Library Name SM155
Species Mus musculus
Strain C57BL/6J
Mutation Wild Type
Location Large intestine - Epithelium
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 large 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 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 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 69

Library Construction

SAGE Protocol SAGE (LongSAGE 21 bp)
Starting RNA 2.5 ug

Tag Extraction

SM155 and SM156 were constructed using the same RNA source, with 2500 ng and 500 ng DNase I treated RNA respectively, ditags were amplified for 27 cycles in both libraries, tags were extracted and correlated.

Merged Library Name SM155_SM156
Total Raw Tags (no quality cut-off) 118,778
Total Raw Tags at Q95 81,396
Total Raw Tags at Q99 79,658
Unique Tags 26,397

Data

Tag Counts at Quality 0.95 cut-off tagcounts-759_SM155_SM156_Q95.txt
Tag Counts at Quality 0.99 cut-off tagcounts-759_SM155_SM156_Q99.txt
Clustered Tag Counts and P-Value tagclustered-759_SM155_SM156.txt
Original Tag Set
Total Raw Tags (no quality cut-off) 71,137
Total Raw Tags at Q95 63,343
Total Raw Tags at Q99 61,619
Unique Tags 19,473

Data

Library Metadata Library Metadata XML
Tag Counts at Quality 0.95 cut-off tagcounts_SM155_Q95.txt
Tag Counts at Quality 0.99 cut-off tagcounts_SM155_Q99.txt
Clustered Tag Counts and P-Value tagclustered_SM155.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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