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Sample GSM869994 Query DataSets for GSM869994
Status Public on Feb 03, 2012
Title iMN-ESCs without Dox treatment, rep1
Sample type SRA
Source name iMN-ESCs, no Dox
Organism Mus musculus
Characteristics background strain: C57BL/6
cell type: inducible motor neurons-embryonic stem cells (iMN-ESCs)
treatment: none
Treatment protocol The ESC aggregates (Ebs) were first treated with all-trans RA (0.5uM) alone for 2 d. Then, RA along-treated Ebs were cultured without or with doxycycline (2ug/mL) in the presence of RA for another 2-3 d.
Growth protocol Mouse iMN-ESCs were trypsinized and grown in ESC growth medium with LIF in suspension as cell aggregates for 2 d.
Extracted molecule total RNA
Extraction protocol The standard Illumina TruSeq RNA Sample Preparation protocol was used with index tags, allowing multiplexing.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description In iMN-ESCs, Isl1-Lhx3 expression is induced upon treatment with doxycycline. iMN-ESCs are derived from mouse ESCs.
Data processing Reads were aligned to the mouse mm9 genome using TopHat. BAM and SAM files were generated as the output files. DEXSeq was used to count the reads per gene based on mm9 RefSeq annotation.
Genome Build:
1doxN.sam.count.txt: mm9
Submission date Feb 02, 2012
Last update date May 15, 2019
Contact name Rongkun Shen
Organization name SUNY Brockport
Department Biology
Street address 350 New Campus Dr
City Brockport
State/province New York
ZIP/Postal code 14420-2997
Country USA
Platform ID GPL13112
Series (1)
GSE35510 Isl1-Lhx3 fusion specifies motor neuron fate by inducing motor neuron genes and concomitantly suppressing the interneuron programs
SRA SRX118412
BioSample SAMN00780188

Supplementary file Size Download File type/resource
GSM869994_1doxN.sam.count.txt.gz 822.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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