|
| Status |
Public on Sep 05, 2019 |
| Title |
WT_LGMP_1 |
| Sample type |
SRA |
| |
|
| Source name |
WT Leukemic GMP cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild type
cell type: Leukemic GMP cells
|
| Treatment protocol |
L-GMP cells were isolated from AMPK WT and KO mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell were sorted into Trizol and RNA were extracted using RNeasy MiniElute Cleanup kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions.
cDNA libraries were generated using the Smart-seq2 protocol. Sequencing libraries were generated from 250 pg of amplified cDNA using Nextera XT kit according to the manufacturer's instructions. Barcoded libraries were purified and sequenced on a NextSeq 500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were mapped to mm10 using STAR, version 2.5.3a, with settings: “alignSJoverhangMin” 8; “alignSJDBoverhangMin” 1; “outFilterMismatchNmax” 999; “alignIntronMin” 20; “alignIntronMax” 1000000; “alignMatesGapMax” 1000000; “twopassMode” Basic; “sjdbOverhang” 100.
FPKM and differential gene expression were calculated with DESeq2 (version 1.18.1) and Ensembl 84 as the reference.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited (TSV) file containing a matrix of FPKM values for all samples
|
| |
|
| Submission date |
Mar 07, 2019 |
| Last update date |
Sep 05, 2019 |
| Contact name |
Daisuke Nakada |
| E-mail(s) |
[email protected]
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Human Genetics
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE127999 |
AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia: RNA-seq |
| GSE128001 |
AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN11082569 |
| SRA |
SRX5492046 |
