SAGE Library SM040

Classification

Library Name SM040
Species Mus musculus
Strain C57BL/6J
Mutation Wild Type
Location Brain - Visual cortex
Sex Male
Age P27
Developmental Stage Post natal day 27
Organsim Condition

Sample Collection

Tissue Dissection Photos

Click to view full-size image…

Schematic of visual cortex dissection from: Gordon, J.A. and M. P. Stryker (1996). “Experience-dependent plasticity of binocular responses in the primary visual cortex of the mouse.” J Neurosci 16(10): 3274-86


Click to view full-size image…

Left side visual cortex dissected, cut out tissue balancing on knife blade.


Click to view full-size image…

1. Left hemisphere cut out depression 2. Dissected visual cortex region (gray matter only) balancing on knife blade.


Click to view full-size image…

Visual cortex dissected out from both brain hemispheres.


Click to view full-size image…

Visual cortex dissected out from both brain hemispheres. Dissected areas outlined in blue.

Creative Commons License
This work is licensed under a Creative Commons Attribution 2.5 License.
Lab CMMT: Elizabeth Simpson
Number of Animals 10

Library Construction

SAGE Protocol SAGELite (LongSAGE 21 bp)
Starting RNA 10.0 ng

Tag Extraction

SM040 and SM073 were constructed using the same RNA source, each with 10 ng DNase I treated RNA, 1st cDNA was amplified with SAGElite PCR for 20 cycles, Ditags were amplified for 25 cycles in LongSAGE protocol, tags were extracted and correlated.

Merged Library Name SM040_SM073
Total Raw Tags (no quality cut-off) 246,517
Total Raw Tags at Q95 168,599
Total Raw Tags at Q99 159,717
Unique Tags 64,102

Data

Tag Counts at Quality 0.95 cut-off tagcounts-898_SM040_SM073_Q95.txt
Tag Counts at Quality 0.99 cut-off tagcounts-898_SM040_SM073_Q99.txt
Clustered Tag Counts and P-Value tagclustered-898_SM040_SM073.txt
Original Tag Set
Total Raw Tags (no quality cut-off) 137,463
Total Raw Tags at Q95 114,280
Total Raw Tags at Q99 107,941
Unique Tags 39,744

Data

Library Metadata Library Metadata XML
Tag Counts at Quality 0.95 cut-off tagcounts_SM040_Q95.txt
Tag Counts at Quality 0.99 cut-off tagcounts_SM040_Q99.txt
Clustered Tag Counts and P-Value tagclustered_SM040.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.