SAGE Library SM124

Classification

Library Name SM124
Species Mus musculus
Strain C57BL/6J
Mutation Wild Type
Location Kidney - Mesenchyme
Sex Unknown
Age E12
Developmental Stage Theiler Stage 20
Organsim Condition

Sample Collection

Tissue Dissection Photos

With the aid of a dissecting microscope, whole kidneys were manually removed from embryos submerged in phosphate buffered saline (PBS). To dissociate the mesenchyme, kidneys were subsequently placed in 500 uL of 1% trypsin in Hanks solution. After 90 minutes of incubation at 4ÂșC, the digestion was stopped with the addition of 1 mL of 20% fetal bovine serum (FBS) in Hanks solution plus a small amount of DNase I powder. Tungsten needles were used to tease away the mesenchyme which was collected in tubes containing Trizol. Tissue from several litters was collected to obtain enough RNA for SAGE library construction. No more than two litters were dissected on the same day, with each litter taking about 1hour to manually dissocitate after trypsin digestion.

Creative Commons License
This work is licensed under a Creative Commons Attribution 2.5 License.
Lab BCCRC: Cheryl Helgason Lab
Number of Animals 77

Library Construction

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

Tag Extraction

Total Raw Tags (no quality cut-off) 113,355
Total Raw Tags at Q95 90,457
Total Raw Tags at Q99 86,180
Unique Tags 39,813

Data

Library Metadata Library Metadata XML
Tag Counts at Quality 0.95 cut-off tagcounts_SM124_Q95.txt
Tag Counts at Quality 0.99 cut-off tagcounts_SM124_Q99.txt
Clustered Tag Counts and P-Value tagclustered_SM124_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.

SAGE Library Help

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