|
| 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 |
| E-mail(s) |
mmacchie@umn.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN03580692 |
| SRA |
SRX1016125 |
