|
| Status |
Public on Dec 19, 2013 |
| Title |
PRMT4-KD2 |
| Sample type |
SRA |
| |
|
| Source name |
cord blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary CD34+ cell
genotype/variation: PRMT4-KD
|
| Treatment protocol |
CD34+ cells were infected with lentiviruses carrying PRMT4KD or scramble control shRNAs in the presence of 8µg/ml polybrene and spin inoculation . Transduced cells were sorted based on GFP positivity 72h after transduction.
|
| Growth protocol |
Purifed human cord blood derived CD34+ cells were cultured in Iscove`s modified Dulbecco`s medium (IMDM, Cellgro) containing 20% BIT 9500 medium (Stem Cell Technologies) supplemented with SCF (100 ng/ml), FLT-3 ligand (10 ng/ml), IL-6 (20 ng/ml) and TPO (100 ng/ml)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy Plus® mini kit (QIAGEN, Germany).
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# RS-122-2001). Briefly, mRNA was purified and fragmented, then synthesized cDNA strand, end-repaired following Illumina standard RNA sample preparation protocols. Libraries were sequenced on Hiseq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Reads were aligned using Tophat 1.4.0 with Bowtie 1
Normalized gene counts were calculated using the DESeq Bioconductor package version 1.10.1 with detault settings
Genome_build: hg19
Supplementary_files_format_and_content: counts_scaled_DESeq.txt is a tab-delimited file containing normalized gene counts for each sample.
|
| |
|
| Submission date |
Apr 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Bic MSKCC |
| Organization name |
Memorial SLoan-Kettering Cancer Center
|
| Street address |
1275 York Ave.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46056 |
RNAseq of PRMT4KD in human cord blood derived CD34+ cells |
|
| Relations |
| SRA |
SRX265383 |
| BioSample |
SAMN02045879 |
