|
| Status |
Public on Aug 22, 2013 |
| Title |
60_exp1 |
| Sample type |
RNA |
| |
|
| Source name |
human MLL-AF4 ALL SEM cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MLL-AF4 ALL SEM
genotype/variation: JMJD1C knock down
|
| Treatment protocol |
For shRNA expression, culture medium was supplemented with 1 mM IPTG (Sigma).
|
| Growth protocol |
SEM Cells were transduced with pLKO-puro-IPTG-3xLacO lentiviral vectors and selected with 2 μg/ml puromycin (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using RNeasy Plus RNA kit (Qiagen) and reverse transcribed using TaqMan Reverse Transcription Reagents (Applied Biosystems).
|
| Label |
biotin
|
| Label protocol |
standard Affymetrix procedure
|
| |
|
| Hybridization protocol |
standard Affymetrix procedure
|
| Scan protocol |
standard Affymetrix procedure
|
| Description |
Gene expression data from MLL-AF4 ALL cell line SEM with JMJD1C knock down
|
| Data processing |
The raw data was first analyzed with Affymetrix Power Tools (APT version: 1.14.4.1, see www.affymetrix.com) to calculate gene level RMA probe set summation values. The APT command was: apt-probeset-summarize -a rma -a rma-bg,quant-norm.sketch=-1.bioc=true.lowprecision=false.usepm=true,pm-only,med-polish.expon=true -a pm-only,dabg.chisq=true -p ${affy_lib}/HuGene-2_0-st.pgf -c ${affy_lib}/HuGene-2_0-st.clf -b ${affy_lib}/HuGene-2_0-st.bgp --qc-probesets ${affy_lib}/HuGene-2_0-st.qcc -m ${affy_lib}/HuGene-2_0-st.mps ${cel_dir}/*.CEL -o ${out_dir}/gene_level. The Affymetrix microarray annotation (HuGene-2_0-st_rev1.zip) was downloaded from http://www.affymetrix.com/support/technical/libraryfilesmain.affx on june 17 2013. All the post-APT processing including filtering, statistical analysis and plotting was done in R.
|
| |
|
| Submission date |
Aug 20, 2013 |
| Last update date |
Aug 22, 2013 |
| Contact name |
Kristian Helin |
| E-mail(s) |
kristian.helin@bric.ku.dk
|
| Organization name |
Copenhagen University
|
| Department |
BRIC
|
| Street address |
Ole Maaløes vej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL16686 |
| Series (1) |
| GSE50048 |
shRNA Screening Identifies JMJD1C as being required for Leukemia Maintenance |
|
