|
| Status |
Public on Apr 10, 2013 |
| Title |
Dicer_Null_2 |
| Sample type |
SRA |
| |
|
| Source name |
Dicer -/- murine MSC cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell type: murine MSC cell line
genotype: Dicer -/-
strain: C57BL/6
rna: small RNA
|
| Treatment protocol |
Monoclonal immortalized Dicer WT and KO MSCs were cultured to near-confluence under normal growth conditions and then harvested for RNA isolation.
|
| Growth protocol |
Monoclonal immortalized MSCs were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiazol reagent according to manufacturer's instructions. 15-50 nt small RNAs were selected from a 15% polyacrylamide TBE-urea gel.
Libraries were cloned and sequenced using the Illumina small RNA-sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Small RNAs (15-50 nts in length) from immortalized monoclonal lines of Dicer-/- (Dicer KO) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, were analyzed.
|
| Data processing |
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Raw reads were processed to remove traces of 3' linker (CTGTAGGCACCATCAAT) and summarized by sequence identity (observations).
Genome_build: mm9
Supplementary_files_format_and_content: Text file with sequence and count
|
| |
|
| Submission date |
Feb 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
A Bhutkar |
| Organization name |
MIT
|
| Street address |
77 Massachusetts Avenue
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE44156 |
Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [small_RNA-Seq] |
| GSE44163 |
Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts |
|
| Relations |
| SRA |
SRX228546 |
| BioSample |
SAMN01915276 |
