|
| Status |
Public on Sep 21, 2017 |
| Title |
RNAseq HpbALL-non-targeting guide_2 |
| Sample type |
SRA |
| |
|
| Source name |
T cell leukemia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HpbALL
cell type: T cell leukemia
|
| Treatment protocol |
long non coding RNA knockdown is achieved by either infecting cells with lentivirus carrying CRISPR components or antisense oligo (ASO) are added directly in cell culture to 1uM
|
| Growth protocol |
cells are growth in RMPI 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extranction is carried out by RNAeasy plus kit
RNAseq library were prepare by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina ( cat #E7420L)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
HBP-NTG-rep2
|
| Data processing |
reads were aligned using STAR aligner v1.4.2 with default parameters
raw counts are calculated by STAR aligner
raw counts were inputed into DESeq2 for differential expression analyiss and normalized count generation
Genome_build: hg19/GENCODE_v19
Supplementary_files_format_and_content: normalized counts in tab delimited file
|
| |
|
| Submission date |
Sep 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Iannis Aifantis |
| E-mail(s) |
iannis.aifantis@nyumc.org
|
| Organization name |
New York University School of Medicine
|
| Department |
Pathology
|
| Lab |
Aifantis Lab
|
| Street address |
550 First Avenue, Smilow Research Building Room 1301
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE104018 |
RNAseq of T-ALL upon long non coding rna purturbation |
|
| Relations |
| BioSample |
SAMN07666494 |
| SRA |
SRX3198163 |
