|
| Status |
Public on Aug 18, 2014 |
| Title |
CUTLL1 carrying a second shRNA targeting LUNAR1_3 |
| Sample type |
SRA |
| |
|
| Source name |
CUTLL1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human T-ALL cell line
cell line: CUTTL1
|
| Growth protocol |
Cell lines were grown in RPMI with 10% FBS, 1X glutamax and 1X pen-strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy kit (Qiagen)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
shLnc2_2
Strand-specific RNA-SEQ (dUTP method)
|
| Data processing |
Basecalls performed using CASAVA
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Differential gene expression analysis was performed using cuffdiffv2.1
Genome_build: hg19
Supplementary_files_format_and_content: TAB-delimited text with FPKM values
|
| |
|
| Submission date |
May 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Trimarchi |
| Organization name |
NYU School of Medicine
|
| Department |
Pathology
|
| Lab |
Iannis Aifantis
|
| Street address |
550 First Ave Smilow 1307
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE57982 |
Transcriptome profiling in human T-ALL |
|
| Relations |
| BioSample |
SAMN02800344 |
| SRA |
SRX553483 |
