|
| Status |
Public on Oct 01, 2015 |
| Title |
NIPBL_Mut2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
genotype: NIPBL-haploinsufficient
cell type: Mouse embryonic fibroblasts
passages: 3
strains: CD1
|
| Growth protocol |
MEFs were grown in DMEM supplemented with 10% fetal bovine serum (FBS). Cells of 3rd passage were used for RNA isolation for sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from mouse ES cells was isolated with TRIzol Reagent (Life Technologies, 15596) following the manufacturer’s instructions. RNA was treated with DNase I (NEB, M0303S) to remove contaminated genomic DNA. After that, RNA was depleted of ribosomal RNA with the Ribo-Zero kit (Epicentre).
The ribo-depleted RNA samples were amplified with the TruSeq RNA Sample Prep Kit (Illumina) for Solexa sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline
Reads from three biological replicates for WT and NIPBL+/- were aligned to the mouse genome UCSC mm10 and to gene annotations from Ensembl 72 using TopHat 2.0.10 using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-Seq RPKM expression values were computed for each gene using edgeR.
|
| |
|
| Submission date |
Jan 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jennifer Gerton |
| Phone |
8169264301
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Gerton Lab
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE64706 |
Transcriptome analysis of mouse embryonic fibroblasts of NIPBL-haploinsufficient mice |
|
| Relations |
| BioSample |
SAMN03276165 |
| SRA |
SRX831399 |
