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Sample GSM3073011 Query DataSets for GSM3073011
Status Public on Oct 18, 2018
Title RNA_C36-TCF3_CHA replicate 2
Sample type SRA
Source name RNA_C36-TCF3_CHA
Organism Mus musculus
Characteristics cell type: pre-B cells Arf-/-
genotype: TCF3-ZNF384 Fusion
strain: C57BL/6
Growth protocol Cells were derived from C57BL/6 Arf-/- BM cells as described (Randle et al, PNAS, 2001). Cells were transduced with lentiviral supernatants of ZNF384-HA, TAF15-ZNF384-HA, or TCF3-ZNF384-HA.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from GFP+ sorted cells using RNeasy Mini Kit (QIAGEN).
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit (Illumina.)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description RNASeq_counts.mm9.txt
Data processing Paired-end 100-cycle sequencing was performed per the manufacturer’s directions (Illumina).
RNA-Seq was mapped as described previously (Downing et al., 2012)
HTSeq (version 0.6.1p1) were used to get gene-level count and estimated FPKM based on GENCODE (vM9).
Genome_build: mm9
Supplementary_files_format_and_content: gene-based rawcounts
Submission date Mar 30, 2018
Last update date Oct 18, 2018
Contact name Beisi Xu
Organization name St Jude Children's Research Hosipital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
Platform ID GPL24247
Series (2)
GSE112558 RNA-sequencing to investigate transcriptional changes caused by ZNF384 fusion proteins in murine pre-B cells
GSE112561 Genomic classification and identification of the cell of origin of pediatric mixed phenotype acute leukemia
BioSample SAMN08824605
SRA SRX3868851

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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