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Sample GSM47340 Query DataSets for GSM47340
Status Public on Apr 04, 2005
Title Brain:Hippocampus, Female (MoBr.FeHi)
Sample type MPSS
 
Source name Brain:Hippocampus, Female total RNA
Organism Mus musculus
Extracted molecule total RNA
 
Description Strain: C57BL6
Brain:Hippocampus, Female total RNA (MoBr.FeHi) received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test. The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4): 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634). Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector. The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library MoBr.FeHi.sig21
Cell type Brain:Hippocampus, Female
Source NHGRI
RNA isolation LYNX mRNA QC passed
cDNA library:
Library DpnII restriction - (signature cloning using MmeI)
Sequence length 20 bp
MPSS:
runs
MoBr.FeHi_sig21.5420F.d-20 3/18/2005 489602 16681 QC Passed
MoBr.FeHi_sig21.5420F.f-20 3/31/2005 399267 12775 QC Passed
MoBr.FeHi_sig21.5420F.g-20 3/31/2005 381118 12185 QC Passed
MoBr.FeHi_sig21.5420W.b-20 2/28/2005 440070 12758 QC Passed
MoBr.FeHi_sig21.5420W.c-20 3/22/2005 495684 18076 QC Passed
MoBr.FeHi_sig21.5420W.d-20 3/28/2005 456966 12301 QC Passed
Run group:
Total Beads successfully sequenced - 2662707
Processed Signatures - 25456
 
Submission date Apr 04, 2005
Last update date Dec 14, 2005
Contact name Daixing Zhou
E-mail(s) dzhou@solexa.com
Phone 510-670-9441
Fax 510-670-9302
URL http://www.solexa.com
Organization name Solexa
Department Bioinformatics
Street address 25861 Industrial Blvd
City Hayward
State/province CA
ZIP/Postal code 94545
Country USA
 
Platform ID GPL1010
Series (1)
GSE1581 MPSS mouse transcriptome analysis project

Data table header descriptions
ID_REF Signature - 20 nt sequence including DpnII site (GATC)
VALUE Mean abundance for a signature derived from all MPSS runs for the sample, in transcripts per million (TPM)
ST_DEV Standard deviation of the mean abundance from multiple MPSS runs
REP Replication_global


Total number of rows: 12507

Table truncated, full table size 368 Kbytes.




Supplementary file Size Download File type/resource
GSM47340.raw.txt.gz 340.5 Kb (ftp)(http) TXT

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