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Sample GSM1673652 Query DataSets for GSM1673652
Status Public on Apr 30, 2019
Title MEL_RNA_D5R1
Sample type SRA
Source name MEL
Organism Mus musculus
Characteristics cell type: MEL
time: D5
Treatment protocol MELs grown to a density of 1 million/ml were differentiated using 2% DMSO (VWR) added to the medium and the cells were grown for another 5 days to induce the expression of hemoglobin genes. At least 80-90% of cells expressed hemoglobin based on their color and benzidine/hydrogen peroxide staining result.
Growth protocol Mouse erythroleukemia cells (MEL, ATCC, Manassas, VA) were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with penicillin/streptomycin (Life Technologies) and 10% FBS (VWR, Radnor, PA). Trypan Blue (VWR) staining was performed before harvesting the cells for each assay in order to make sure that at least 90% of the cells were viable. All experiments were done with 2 biological replicates.
Extracted molecule total RNA
Extraction protocol MEL total RNA was extract by RNeasy Kit (QIAGEN) and the quality was checked by RIN.
Biological replicates of stranded RNA-seq were built as previously described (Parkhomchuk et al. 2009). The cDNA was ligated to Nextflex DNA barcodes (Bioo Scientific, Austin, TX) compatible with Illumina Sequencing platform and the fraction of the ligation product between 300-350bp (corresponding to 175-225bp insert size) was selected by gel electrophoresis.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description processed_data_file: MEL_RNA_seq_merged_fpkm.txt
Data processing Reads were trimmed to 50bp and mapped by Bowtie with mouse Gencode M1 transcriptome excluding all small RNAs as reference using the settings -aS --offrate 1 -v 3.
Transcription expression levels were determined by eXpress.
genome build: mm9, GENCODE M1 transcriptome
processed data files format and content: merged fpkm matrix file generated by eXpress
Submission date May 03, 2015
Last update date May 15, 2019
Contact name Marissa Macchietto
Organization name University of Minnesota, Minneapolis
Department Minnesota Supercomputing Institute
Street address 117 Pleasant Street SE
City Minneapolis
ZIP/Postal code 55455
Country USA
Platform ID GPL19057
Series (1)
GSE67955 The landscape of global-long range interactions in mouse and human blood cell lines mediated by Yy1, GATA1, and CTCF during differentiation
BioSample SAMN03580692
SRA SRX1016125

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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