|
| Status |
Public on Mar 26, 2024 |
| Title |
mESC Wt1 KO, Dox24 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola
genotype: Wt1 KO
cell type: embryonic stem cells
treatment: induced with dox for 24 hours
|
| Treatment protocol |
ES cells were treated with 1µm retinoic acid or 1µg/ml doxycycline as per the conditions mentioned.
|
| Growth protocol |
Embryonic stem cells were maintained on 0.1% gelatin coated dishes, maintained in GMEM reconstituted with NEAA, sodium pyruvate, 10% FCS, LIF and β-mercaptoethanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the cells using the Qiagen miRNeasy column as per the manufacturers protocol
Total RNA equivalent to 1µg was ligated with the 3’ RNA adapter with the help of the T4 RNA ligase 2 (deletion mutant) followed by ligation of the 5’ RNA adapter using T4 RNA ligase. The adapter ligated RNA was then subjected to reverse transcription with Superscript II RT followed by PCR amplification. The amplified cDNA was electrophoresed on a 6% PAGE gel. Mature microRNA, which is approximately 22 bp, gives an adapter ligated fragment of approximately 147 bp. A second band of 157 bp corresponding to piRNAs, other small noncoding RNA arising from 30 bp small RNAs was also excised together to give rise to the pool of small RNA.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Small RNA
|
| Data processing |
The abundance of mature mouse miRNA from miRBase (http://www.mirbase.org) was quantified using mirna_soft (http://seidman.med.harvard.edu/fgs/software/mirna_soft/mirna_soft.tar.gz) PMCID: PMC4138881.
Supplementary_files_format_and_content: tab separated file with counts per miRNA
|
| |
|
| Submission date |
Mar 26, 2021 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Ruthrothaselvi Bharathavikru |
| E-mail(s) |
brselvi@iiserbpr.ac.in
|
| Phone |
+91 680 2227774
|
| Organization name |
Indian Institute of Science Education and Research
|
| Department |
Biological Sciences
|
| Lab |
RNP Biology Lab
|
| Street address |
IISER Berhampur, Transit Campus
|
| City |
Berhampur |
| State/province |
Odisha |
| ZIP/Postal code |
760010 |
| Country |
India |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE169684 |
MicroRNA profiling of Wilms Tumour 1 deleted and induced embryonic stem cells |
|
| Relations |
| BioSample |
SAMN18499643 |
| SRA |
SRX10450462 |
