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Sample GSM1577178 Query DataSets for GSM1577178
Status Public on Oct 01, 2015
Title NIPBL_Mut3
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
BioSample SAMN03276166
SRA SRX831400

Supplementary file Size Download File type/resource
GSM1577178_NIPBL_Mut3.txt.gz 748.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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