|
| 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 |
|
| Relations |
| SRA |
SRX118412 |
| BioSample |
SAMN00780188 |
