|
| Status |
Public on Oct 18, 2018 |
| Title |
RNA_C31-ZNF384WT-CHA replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
RNA_C31-ZNF384WT-CHA
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pre-B cells Arf-/-
genotype: ZNF384 Wild Type
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
counts.RNA_C31-ZNF384WT-CHA-Rep3b
|
| 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 |
| E-mail(s) |
[email protected]
|
| 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 |
|
| Relations |
| BioSample |
SAMN08824610 |
| SRA |
SRX3868846 |
