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Sample GSM1863149 Query DataSets for GSM1863149
Status Public on Aug 23, 2017
Title CUTLL ICN1 2 [lncRNA]
Sample type SRA
 
Source name CUTLL ICN1
Organism Homo sapiens
Characteristics cell line: CUTLL1
cell type: T-ALL cell line containing a t(7;9) rearrangement and aberrant NOTCH1 activation
passage: <20
treatment: highDBZ_ICN
Treatment protocol Cells transduced with ICN1 and R1984A were maintained in the presence of gamma-secretase inhibitor GSI ((S)-2-[2-(3,5-difluorophenyl)-acetylamino]-N-((S)-5-methyl-6-oxo-6,7-dihydro-5H-dibenzo[b,d]azepin-7-yl)-propionamide, DBZ) at the concentration of 1µM.
Growth protocol Human T-LL cell line CUTLL1 cells were maintained in RPMI1640 medium complement with 10% fetal bovine serum, 1X Penicillin-Streptomycin-Glutamine (PSG).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with RNAeasy kit,
and after ribosomal RNA depletion, stranded RNA libraries were prepared following the instruction of Truseq library preparation guide (Illunima # 15031048). Quality control was assessed by BioA analysis (Agilent Technologies) prior to library construction and again prior to sequencing
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Description genes_10495_rpkm.txt
lncRNA_12606.txt
Data processing Sequence reads were aligned to the hg19 genome using TopHat or Trinity
lncRNA expression levels were identified using Trinity
Genome_build: hg19
Supplementary_files_format_and_content: [lncRNA_12606.txt] lncRNA expression RPKM table processed with Trinity
 
Submission date Aug 28, 2015
Last update date May 15, 2019
Contact name Chongzhi Zang
Organization name University of Virginia
Street address P. O. Box 800717
City Charlottesville
State/province VA
ZIP/Postal code 22908
Country USA
 
Platform ID GPL11154
Series (1)
GSE72482 Sequence dependency and regulatory function of dimeric NOTCH1/RBPJ complexes on coding and non-coding transcription in T-lymphoblastic leukemia
Relations
Reanalysis of GSM1863096
BioSample SAMN04017500
SRA SRX1167288

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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