|
| Status |
Public on Sep 09, 2013 |
| Title |
ME-1 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
ME-1 (leukemic)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: leukemic cell line
cell line: ME-1
treatment: none
|
| Treatment protocol |
U937 CBFβ-MYH11 cells were maintained in the presence of tetracyclin and grown in the absence of tetracycline for induction of CBFβ-MYH11. shRNA expression was induced in ME-1 using dox.
|
| Growth protocol |
ME-1 cells were cultured in normal cell culture containing 10% serum. U937 cells were cultured in tet free culture media for maintenance.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using qiagen RNeasy kit according to manufacturer instructions and total RNA was treated using Ribo-zero to remove rRNA according to manufacturer instructions.
Libraries were prepared according to Illumina's standard protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-seq
|
| Data processing |
Basecalls performed using CASAVA
Reads were aligned to the hg18 or hg19 genome assembly (see characteristics) using ELAND/BWA
Peaks were called using MACS 1.3.3 on settings:mfold =8, tsize=32, p value = e-6
Genome_build: hg18
Supplementary_files_format_and_content: wig or bedgraph files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps
|
| |
|
| Submission date |
Apr 15, 2013 |
| Last update date |
Nov 11, 2021 |
| Contact name |
Joost Martens |
| E-mail(s) |
[email protected]
|
| Phone |
0243780645
|
| Organization name |
Radboud University
|
| Department |
RIMLS
|
| Lab |
Molecular Biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| State/province |
Nederland |
| ZIP/Postal code |
6525GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46044 |
A compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupy CBF-MYH11/RUNX1 target genes |
|
| Relations |
| SRA |
SRX265244 |
| BioSample |
SAMN02045678 |
