NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1874432 Query DataSets for GSM1874432
Status Public on Apr 05, 2016
Title ALL parental replicate B
Sample type SRA
 
Source name Ph+ ALL cells
Organism Mus musculus
Characteristics treatment: none
Treatment protocol Cells were plated at 0.5 million cells/mL and treated at desired drug concentrations. Cells were monitored each day. Upon outgrowth (i.e. cell density reaching 4-5 million cells/mL), cells were 1) frozen down, 2) allowed to recover in no-drug medium, or 3) plated again at 0.5 million cells/mL and treated at the next drug dose. For cells in drug-selection condition, medium was changed every week.
Growth protocol Murine derived Ph+ALL cell line containing BCR-ABL1 p185 was cultured in RPMI medium supplemented with 10% FBS, 4 mM L-glutamine, 5 μM β-mercaptoethanol.
Extracted molecule total RNA
Extraction protocol RNA was extracted using QIAshredder and RNeasy Kit (Qiagen).
Quality of RNA was assessed with BioAnalyzer (Agilent Technologies) and library was prepared with Illumina TruSeq.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 150317Hem_D15_1892
Data processing Basecalls performed using CASAVA v1.7.0
Reads were trimmed to remove adapters and low quality reads using Trimmomatic v0.33
Alignments (to mm9) were performed using TopHat v2.0.12 with the following parameters: --no-novel-juncs --segment-length 20 --read-realign-edit-dist 0. ABL1 was aligned to NM_005157.5 separately using BWA v0.7.10
Differential expression was performed as follows: BAM files sorted and indexed using SAMtools, reads were counted using HTSeq v0.6.1, and differential expression analyses were performed using DESeq R package
Genome_build: mm9
Supplementary_files_format_and_content: expression counts from HTSeq
 
Submission date Sep 10, 2015
Last update date May 15, 2019
Contact name Boyang Zhao
Organization name MIT
Street address 500 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL19057
Series (1)
GSE72910 Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution
Relations
BioSample SAMN04045519
SRA SRX1220456

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap