|
| Status |
Public on Mar 31, 2017 |
| Title |
NBM cells IL4 rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
NBM cells IL4
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
tissue: Mouse normal bone marrow
cell type: c-Kit enriched normal bone marrow
grown in: 20 ng/mL IL3 and IL4 for 18hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow of leukemic or healthy mice were crushed followed by CD117 selection (Miltenyi Biotec, Bergisch Gladbach, Germany). RNA was extracted using the QIAshredder and RNeasy Microkit (QIAgen, Hilden, Germany). Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: NBM_IL4_TMM.txt
|
| Data processing |
Bcl2FastQ software was used for basecalling.
Sequenced reads were mapped to the mm10 referece genome using Tophat 2.0.13 with parameters -p 2 --keep-fasta-order --bowtie1 --no-coverage-search
BAM files were imported to the Qlucore Omics Explorer 3.0 software and normalized using the TMM (Trimmed Mean of M-values) method.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited .txt file of TMM values for all samples
|
| |
|
| Submission date |
Mar 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Pablo Peña-Martínez |
| E-mail(s) |
pablo.pena@med.lu.se
|
| Organization name |
Lund University
|
| Department |
Clinical Genetics
|
| Street address |
Klinikgatan 28
|
| City |
Lund |
| ZIP/Postal code |
22184 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE79068 |
Interleukin 4 induces apoptosis of acute myeloid leukemia cells in a Stat6-dependent manner |
|
| Relations |
| BioSample |
SAMN04544522 |
| SRA |
SRX1624445 |
