|
| Status |
Public on Aug 31, 2018 |
| Title |
Dox_chr_3 (6) |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cells: ESC doxycycline-inducible expressing HA-Flag-AGO2
passages: 8-15
fraction: chromatin
|
| Treatment protocol |
15 h before cell harvesting, transgene expression was induced with 2.5 ug/ml doxycycline in ESC.
|
| Growth protocol |
ESC were grown on 0.1% gelatin in DMEM supplemented with 15% heat-inactivated FBS, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1mM Sodium Pyruvate and 1000 U/ml recombinant leukemia inhibitory factor.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were fractionated and the cytoplasmic and nucleoplamic fractions disgarded. The purified chromatin fraction was resuspended in TRIzol and the chromatin bound RNA isolated.
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Chr_dox_noDox_gene_exp.xlsx
|
| Data processing |
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the mm10 genome using TopHat
Abundance measurements in cuffdiff output
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file reports RPKMs and log2fold change of average RPKM between noDox and Dox
|
| |
|
| Submission date |
Jan 05, 2018 |
| Last update date |
Aug 31, 2018 |
| Contact name |
Markus Hafner |
| E-mail(s) |
Markus.hafner@nih.gov
|
| Phone |
3014026956
|
| Organization name |
NIH
|
| Department |
NIAMS
|
| Lab |
Markus Hafner
|
| Street address |
50 South Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE108800 |
Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [6_chr_seq] |
| GSE108801 |
Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation |
|
| Relations |
| BioSample |
SAMN08296083 |
| SRA |
SRX3534039 |
