|
| Status |
Public on Feb 06, 2017 |
| Title |
Ik1 wild-type 12h DOX rep2 |
| Sample type |
SRA |
| |
|
| Source name |
PDX2 Ik6 pre-B ALL + TET-Ik1
|
| Organism |
Homo sapiens |
| Characteristics |
cell-line: pre-B ALL xenograft
genotype/variation: Ik6,BCR-ABL
induction time: 12 hour
treatment: IK1
|
| Treatment protocol |
Cell suspensions were either untreated or treated with doxycycline (DOX) for the indicated time, prior to sorting cells based on GFP signal
|
| Growth protocol |
Single cell suspensions were prepared from in vitro cell cultured cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRI Reagent (Molecular Research Center, Inc.) followed by purification with an RNeasy kit (Qiagen), or direct isolation by RNA-isolation kit (Qiagen and Macherey-Nagel), with on-column RNase-free DNase I treatment. 1 ug of total RNA was depleted of rRNA using RiboErase (KAPA Biosystems).
RNA libraries were prepared for sequencing using the Kapa Biosystems Kapa Stranded RNA-seq library kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
human_matrix_counts.txt
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor and low-quality sequences, then mapped to hg19 reference genome using tophat2 (Kim et al., 2013 PMID: 23618408) with parameters -p 16 --no-coverage-search, also -G parameter was used in conjunction with the Gencode annotation gtf file (gencode.v23.annotation.gtf)
Uniquely mapped reads were counted using Htseq-counts version v0.6.0 with the parameters -m union -r pos -i gene_name -a 10 --stranded=yes
Genome_build: hg19
Supplementary_files_format_and_content: matrix of normalized HTSeq-counts
|
| |
|
| Submission date |
Nov 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Seth Frietze |
| E-mail(s) |
[email protected]
|
| Phone |
8026560569
|
| Organization name |
University of Vermont
|
| Department |
BHSC
|
| Street address |
106 Carrigan Drive
|
| City |
Burlington |
| State/province |
VT |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE90659 |
Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre-B ALL [RNA-seq] |
| GSE90670 |
Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre-B ALL |
|
| Relations |
| BioSample |
SAMN06068249 |
| SRA |
SRX2381923 |
