|
| Status |
Public on Dec 01, 2023 |
| Title |
S6_Gfi_36N_MLL_AF9_1 |
| Sample type |
SRA |
| |
|
| Source name |
Bonemarrow cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Leukemic bonemarrow cells
genotpye: GFI1 36N /36N
strain: C57BL/6
treatment: Untreated
|
| Treatment protocol |
In case of the temozolomide (TMZ) treated samples: leukemic bone marrow cells were treated with 50 µg/ml temozolomide 20 h before RNA isolation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 5x106 total bone marrow cells of leukemic mice using RNeasy Mini Kit (74104, Qiagen, Germany) as per manufacturer instructions.
The samples were sent to core facility genomics (CFG MFM) in University Hospital Münster for library preparation and sequencing. The NEBNext Poly(A) mRNA Magnetic Isolation module (NEB #E7490) protocol was used for library preparation. Module (NEB #E7490)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
normalized_counts_Gfi1_36N.txt
|
| Data processing |
Transcript quantification was done using Salmon against cDNA sequences of mouse genome assembly mm10.
ComBat-seq was used to adjust the batch effect in the case of two batches.
Read count normalization was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files and normalised read counts
|
| |
|
| Submission date |
Feb 02, 2022 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Pradeep Kumar Patnana |
| E-mail(s) |
pradeep.patnana@gmail.com
|
| Organization name |
University Hospital Muenster
|
| Street address |
Domagkstr 3
|
| City |
Muenster |
| State/province |
NRW |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE195955 |
Trancriptomic analysis of leukemic bone marrow cells with GFI1 wildtype, GFI1 SNP variant (GFI1-36N) and low level of GFI1 expression |
|
| Relations |
| BioSample |
SAMN25596621 |
| SRA |
SRX14018429 |
