Transcriptomics

Dataset Information

2

Mus musculus hematopoietic stem cell


ABSTRACT: 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. 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.

ORGANISM(S): Mus musculus  

SUBMITTER: Young-Hun Kim   Hyeng-Soo Kim  Junmo Hwang  Ji-Hong Ha  Jae-Woong Lee  Kyu-Tae Chang  Seonggon Kim  Jin-Woong Chung  Kil-Soo Kim  Zae-Young Ryoo  Sanggyu Lee 

PROVIDER: E-GEOD-16139 | ArrayExpress | 2009-05-20

SECONDARY ACCESSION(S): GSE16139PRJNA115041

REPOSITORIES: GEO, ArrayExpress

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Publications

Detection of low-abundant novel transcripts in mouse hematopoietic stem cells.

Kim Hyeng-Soo HS   Hwang Junmo J   Kim Young-Hun YH   Kim Seonggon S   Lee Jae-Woong JW   Kang Hyung-Sik HS   Kim Kil Soo KS   Ha Ji-Hong JH   Chung Jin Woong JW   Chang Kyu-Tae KT   Ryoo Zae Young ZY   Lee Sanggyu S  

Molecular genetics and genomics : MGG 20090708 4


Gene expression profiles of hematopoietic stem cells (HSCs) provide clues for understanding molecular mechanisms of HSC behavior, including self-renewal and differentiation. We took advantage of serial analysis of gene expression (SAGE) to identify medium- and low-abundant transcripts expressed in HSCs/hematopoietic progenitor cells (HPCs). Among a total of 31,380 unique transcripts, 17,326 (55%) correspond to known genes and, 14,054 (45%) are low-copy transcripts that have no matches to current  ...[more]

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