|
| Status |
Public on Apr 27, 2015 |
| Title |
6hrs_RA_2 |
| Sample type |
SRA |
| |
|
| Source name |
KH2 cells, 6 hrs RA
|
| Organism |
Mus musculus |
| Characteristics |
cell type: KH2 cells
treatment: 6 hrs RA
passages: 12
|
| Treatment protocol |
Feeders were separated by plating freshly trypsinized cells on gelatinized plate for 30 min. After half an hour media was aspirated and centrifuged for 5 min at 1000 rpm.
ES Cells were differentiated with differentiation media (DMEM + 10% Serum + NAA+ 0.03µM RA) RA supplemented 33nm for requisite length of time.
|
| Growth protocol |
Cells were grown in ES cell media (DMEM + 15% Serum + NAA+ Beta-mercaptoethanol)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in TRIzol and RNA was isolated using Directzol RNA miniprep kit( R2052). Quality of RNA were assessed using bioanalyzer and samples with RIN more than 9 were used for library preparation.
For each sample, 250ng of total RNA was used to make libraries. Following manufacturer's directions, short fragment libraries were made using the Illumina TruSeq Stranded Total RNA LT - (with Ribo-Zero TM Gold) - set A and B (Illumina, Cat. No. RS-122-2301 and RS-122-2302). The resulting libraries were quantified using the LabChip GX (Perkin Elmer) and a Qubit Fluorometer (Life Technologies). All libraries were pooled, quantified and run as 50 bp single read on an Illumina HiSeq 2500 instrument using HiSeq Control Software 2.2.58
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequences were aligned to mouse genome mm10 using tophat with default parameters.
Transcript definitions were according to Ensembl 75.
Data was analyzed using Bioconductor package EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: cufflinks gene level results
|
| |
|
| Submission date |
Apr 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Madelaine Gogol |
| Organization name |
Stowers Institute
|
| Department |
Computational Biology Core
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE61590 |
Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters |
| GSE67610 |
Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters. |
|
| Relations |
| BioSample |
SAMN03462080 |
| SRA |
SRX978944 |
