The Brain!
Melbourne Brain Genome Project

Data

This webpage enables the retrieval of SAGE data. Data that has yet to be published has restricted access. Published data will be made freely available. Data can be retrieved in bulk as chromatograms (where available), sequence files, SAGE tags and their respective abundances, and TAGBANK.sum files for use in SAGE2000. All of the sequence files have been formated for use in SAGE2000. In cases where the number of chromatograms available is greater than the number of sequence files available, unfortunately these sequences were complete failures and cannot be extracted from the raw data file. For these files, the only possibility is manual base scoring.
Note: when using SAGE2000 to extract tags from the sequence files, make sure that the stop position includes the length of the longest sequence. The sequence files should be ASCII text, with very long lines, with no line terminators.

Name
of
library
Description
Protocol
used
Tissue
Age
of
mice
Genotype
Chromatograms?
Sequence files?
Tags and counts
Phred scores and SAGE2000 files
Submitter
ADNorWB11m
 
I-SAGE kit
Whole brain
11 months
C57/BL6 crossed with CHOW (parental cross)
1632 chromatograms (280,968 KB) 1632 sequence files [PHRED] (959 KB) 58,004 tags, 20,054 unique tags
5564 duplicate dimers
Phred scores
TAGBANK.sum
Monica Brown
[Contact ].
ADmuWB11m
 
I-SAGE kit
Whole brain
11 months
C57/BL6 crossed with CHOW (parental cross)
1536 chromatograms (277,069 KB) 1536 sequence files [PHRED] (900 KB)
1536 sequence files [ABI] (859 KB)
47,128 tags, 401 duplicate dimers [ABI]
46,977 tags, 383 duplicate dimers [PHRED]
 
[Contact .
DabMuCCE17
A mouse model with the disabled homolog 1 (Dab1, mdab1) gene knocked out [See the DabWTcce17 library]
I-SAGE kit
Cerebral cortex
E17.5
Dab-/-
1920 chromatograms (175,460 KB)
1920 sequence files [PHRED] (891 KB)
1920 sequence files [ABI] (820 KB)
44272 tags
997 duplicate dimers [ABI]
47564 tags
1107 duplicate dimers [PHRED]
Phred scores TAGBANK.sum [ABI]
TAGBANK.sum [PHRED]
DabWTCCE17
A wild-type mouse containing the disabled homolog 1 (Dab1, mdab1) gene [See the DabMucce17 library]
Original protocol
Cerebral cortex
E17.5
Dab +/+
Library two 384 chromatograms (35,029 kb)
Library three 1056 chromatograms (188,164 kb)
Library two 384 sequence files (PHRED) (175 kb)
Library two 384 sequence files (ABI) (162 kb)
Library three 1053 sequence files (ABI) (610 kb)
Library three 1053 sequence files (PHRED) (644 kb)
Library two : 13804 tags, 315 duplicate dimers [PHRED]
Library two : 12519 tags, 243 duplicate dimers [ABI]
Library three : 47912 tags, 280 duplicate dimers [ABI]
Library three : 45363 tags, 243 duplicate dimers [PHRED]
TAGBANK.sum Library 2 [PHRED]
TAGBANK.sum Library 2 [ABI]
TAGBANK.sum Library 3 [ABI]
TAGBANK.sum Library 3 [PHRED]
E15 anterior neocortex
 
Original protocol
Anterior cortex
E15.5
C57/BL6
No chromatograms are available for this library.
1665 sequence files
Tags and counts
31585 tags
3944 duplicate dimers
 
E15 posterior neocortex
 
Original protocol
Posterior cortex
E15.5
C57/BL6
     
2906 sequence files
Tags and counts
39314 tags
435 duplicate dimers.
BL6SCN
 
I-SAGE kit
Neurosphere cells
 
 
     
1920 chromatograms (176694 KB)
Phred scores
2207 sequence files (986 KB)
Tags and counts
48329 tags
1885 duplicate dimers
B6 HypoThal
 
Original protocol
Hypothalamus
8 weeks
C57/BL6
    78784 tags
1946 duplicate dimers
8735 chromatograms (plus one miscellaneous file) (820,442 KB)
phred scores
8735 sequence files (5,045 KB) 78784 tags, 1946 duplicate dimers (SAGE2000).
B6 HypoThalSD
 
Original protocol
Hypothalamus
8 weeks
C57/BL6
   
77909 tags, 2644 sequence files, 948 duplicate dimers
2644 sequence files (extracted using phred).
2644 chromatograms
77909 tags
948 duplicate dimers
B6 HypoThalSR
 
Original protocol
Hypothalamus
8 weeks
C57/BL6
4603 chromatograms (261,229 KB)  
 
51194 tags, 765 duplicate dimers (SAGE 2000, ABI).
"4603 chromatograms "4605 sequence files
P1 neocortex
 
Original protocol/I-SAGE kit
Cerebral cortex
PN1.5
C57/BL6
     
"4194 sequence files
" 42869 tags. 1829 duplicate dimers.
E15 neocortex
 
Original protocol/I-SAGE kit
Cerebral cortex
E15.5
C57/BL6
 
4425 sequence files
62142 tags, 23724 unique tags, 2350 duplicate dimers
NeoLHAdLS1
 
Long SAGE
Neocortex left side
5-6 months
C57/BL6
2880 chromatograms (348,449 KB)
2880 sequence files [PHRED] (1,618 KB)

2871 sequence files [ABI] (1,478 KB)
15,611 unique 10 bp tags, 30,385 tags in total [PHRED]
17,684 unique 17 bp tags, 30,480 tags in total 4113 duplicate dimers [PHRED]
15,057 unique 10 bp tags, 29,814 tags in total [ABI]
17,790 unique 17 bp tags, 30,634 tags in total 4135 duplicate dimers [ABI]
 
Monica Brown.
[Contact ]
NeoRHAdLS
 
Long SAGE
Neocortex right side
5-6 months
C57/BL6
2784 chromatograms (486,986 kb)
2782 sequence files (PHRED) (1,661 KB)
2779 sequence files (ABI) (1,557 KB)
22,076 unique 10 bp tags, 50,755 tags in total [PHRED]
24,977 unique 17 bp tags, 50,842 tags in total [PHRED] 6598 duplicate dimers
21,903 unique 10 bp tags, 50,941 tags in total [ABI]
25,069 unique 17 bp tags, 51,254 tags in total [ABI] 6656 duplicate dimers
 
Violetta Spirkoska.
[Contact
NeoRHAdLS1
 
Long SAGE
Right hemisphere of cerebral cortex
6 months
C57/BL6
1920 chromatograms (346, 564 KB)
1920 sequences (1,111 KB) [PHRED]
1911 sequences (1,160 KB) [ABI]
19,260 unique 10 bp tags, 39,354 tags in total [PHRED]
22,688 unique 17 bp tags, 39,426 tags in total[PHRED]
19,079 unique 10 bp tags, 39,306 tags in total [ABI]
22,483 unique 17 bp tags, 39,306 tags in total 2994 duplicate dimers [ABI]
 
Monica Brown.
[Contact
Ts65Dn
 
Original protocol
Brain
 
 
     
"SAGE 10 base pair tags and counts file for normal male, normal female and male Ts65Dn. (901 KB)
50726 tags for normal male, 50504 tags for normal female, and 51561 tags for Ts65Dn male.
R1 Embryonic Stem Cells
 
SAGE
R1 ES cells, undifferentiated
 
 
     
"GSM580
" 137906 tags.
Kenneth R. Boheler : [email protected]
Pubmed_id = 11829487
National Institute on Aging, NIH
Laboratory of Cardiovascular Science
GRC
5600 Nathan Shock Drive
Baltimore,MD,21224,USA
http://www.grc.nia.nih.gov/branches/lcs/mcu.htm
Platform_id = GPL11
3T3 cells, hypothalamus, P10.5 crx-/-, P10.5 crx+/+, adult whole retina and adult microdissected outer nuclear layer (ONL)
 
SAGE
3T3 cells, hypothalamus, P10.5 crx-/-, P10.5 crx+/+, adult whole retina and adult microdissected outer nuclear layer (ONL)
 
 
     
3T3 cells, hypothalamus, P10.5 crx-/-, P10.5 crx+/+, adult whole retina and adult microdissected outer nuclear layer (ONL)
"Table S2. SAGE tag levels for nonretinal, P10.5, adult retina, and ONL libraries This lists a full breakdown of all SAGE tags from the following libraries: 3T3 cells, hypothalamus, P10.5 crx-/-, P10.5 crx+/+, adult whole retina and adult microdissected outer nuclear layer (ONL). Tag totals are normalized to 55,000. The Gene field contains the mouse Unigene number assignment for the tag followed by the gene name. Tags with multiple predicted identities are listed together in the Gene column."
Adult and Hypothalamus data
 
Adult and Hypothalamus
 
 
No chromatograms available.
3268 sequence files ( kb)
ADULT : 49046 tags, 3453 duplicate dimers
TAGBANK.sum


When comparing SAGE libraries generated from different strains, to check for polymorphisms in your gene(s) of interest that may differ between the libraries, you can use the Polymorphisms Query Form in the Mouse Genome Database (http://www.informatics.jax.org/sea rches/polymorphism_form.shtml) to search for reported differences between strains. To do this
1. go to the query form at the URL above
2. enter the strain into the Primary Strain(s) field, leaving "begins" as the operator
3. select the Chromosome of choice and press the "Retrieve" button.
A list of known polymorphisms at markers and genes on the chromosome between the strain selected and other strains will be returned.

A collection of SAGE libraries enables subtraction to create specific lists, e.g. cortex specific transcripts.


Last modified on the 27th February 2003.
Website comments or suggestions for additional data to