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Series GSE16139

Query DataSets for GSE16139

Status

Public on May 20, 2009

Title

Mus musculus hematopoietic stem cell

Organism

Mus musculus

Experiment type

Expression profiling by SAGE

Summary

A transcriptome study in mouse hematopoietic stem cells was performed using a sensitive SAGE method, in an attempt to detect medium and low abundant transcripts expressed in these cells. Among a total of 31,380 unique transcript, 17,326 (55%) known genes were detected, 14,054 (45%) low-copy transcripts that have no matches to currently known genes. 3,899 (23%) were alternatively spliced transcripts of the known genes and 3,754 (22%) represent anti-sense transcripts from known genes.

Overall design

Mouse hematopoietic stem cells were purified from bone marrow cells using negative and positive selection with a Magnetic-Activated Cell Sorter (MACS). total RNA and mRNA were purified from the purified cells using Trizol reagent and magnetic oligo dT beads. Double strand cDNAs were synthesized using a cDNA synthesis kit and anchored oligo dT primers. After NlaIII digestion, 3’ cDNAs were isolated and amplified through 16-cycle PCR. SAGE tags were released from the 3’ cDNA after linker ligation. Ditags were formed, concatemerized and cloned into a pZERO vector. Sequencing reactions were performed with the ET sequencing terminator kit. Sequences were collected using a Megabase 1000 sequencer. SAGE tag sequences were extracted using SAGE 2000 software.

Contributor(s)

Kim H, Hwang J, Kim Y, Kim S, Lee J, Kim K, Ha J, Chung J, Chang K, Ryoo Z, Lee S

Citation(s)

19585147

Submission date

May 17, 2009

Last update date

Mar 21, 2012

Contact name

Sanggyu Lee

E-mail(s)

[email protected]