|
| Status |
Public on Jun 09, 2022 |
| Title |
RNAseq_KLF4_OE |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow derived lineage-negative cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Lin-
vector: KLF4_OE
|
| Growth protocol |
Cells have been growth in STEM span medium cytokine enriched and then spin-infected with KLF4-retroviral vectors. After 48 hours, GFP positive cells have been sorted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: RNA extraction was performed using the miRNA kit (Qiagen) following manufacturer’s instruction.
Libraries were prepared according to Illumina instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq analysis: Alignment: Sequence of the reads of the samples were mapped to the mouse genome (mm10) using TOPHAT (PubMed ID 22383036) with the option -g 1.
SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each RNA-seq experiment. Height of the profiles was normalized by the total number of reads mapped over the mouse genome.
Assembly: mm10
Supplementary files format and content: Files *.bdg.gz (BedGraph, genome-wide RNA-seq)
Supplementary files format and content: RNAseq_KLF4_OE.bedgraph.gz
Supplementary files format and content: RNAseq_KLF4-PMLRAR_OE.bedgraph.gz
|
| |
|
| Submission date |
Mar 08, 2022 |
| Last update date |
Jun 10, 2022 |
| Contact name |
Enrique Blanco |
| E-mail(s) |
enrique.blanco@crg.eu
|
| Phone |
+34 93 316 01 00
|
| Organization name |
Center for Genomic Regulation (CRG)
|
| Department |
Gene Regulation, Stem Cells and Cancer
|
| Lab |
Epigenetic Events in Cancer (L. Di Croce's lab)
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE151837 |
PML-RARa induces dynamic changes in genome architecture during leukemic transformation |
|
| Relations |
| BioSample |
SAMN26524878 |
| SRA |
SRX14434447 |
