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Mus musculus

ABSTRACT: RNA sequencing of LPS treated mouse bone marrow stromal cells

PROVIDER: PRJNA271325 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1736630.fastq.gz	Fastqsanger.gz
	SRR1736631.fastq.gz	Fastqsanger.gz
	SRR1736632.fastq.gz	Fastqsanger.gz
	SRR1736633.fastq.gz	Fastqsanger.gz
	SRR1736628.fastq.gz	Fastqsanger.gz

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Project description: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.

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