|
| Status |
Public on Nov 23, 2016 |
| Title |
AF9 ALL-1 |
| Sample type |
SRA |
| |
|
| Source name |
CD34+ HSPCs
|
| Organism |
Homo sapiens |
| Characteristics |
lineage: lymphoid
genotype: MLL-AF9
cell etiology: UCB
|
| Growth protocol |
Lymphoid cells were extracted from mouse bone marrow, red blood cells were lysed. Myeloid culture cells were maintaind in IMDM with 10% FBS and 10ng/mL of SCF, TPO, Flt3 ligand, IL-3 and IL-6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted. Total RNA was isolated from sorted cells using RNeasy Mini Kit (Qiagen).
PrepX mRNA Library kit (WaferGen) was used with 1 ug of total RNA for the construction of sequencing libraries, the libraries were clustered by using IIIumina TruSeq PE Cluster kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
processed data file: ALL Af4_vs_AF9 all gene result.txt
|
| Data processing |
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: hg19
Supplementary_files_format_and_content: DESeq output with appended columns containing RPKM values for samples.
|
| |
|
| Submission date |
Jan 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shan Lin |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
EHCB
|
| Lab |
James Mulloy
|
| Street address |
3333 Burnet Avenue, CCHMC
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE76978 |
A faithful in vivo model of human MLL-AF4 proB acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN04421978 |
| SRA |
SRX1534862 |
