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Status |
Public on Apr 05, 2016 |
Title |
ALL parental replicate B |
Sample type |
SRA |
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Source name |
Ph+ ALL cells
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Organism |
Mus musculus |
Characteristics |
treatment: none
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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.
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
150317Hem_D15_1892
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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
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Submission date |
Sep 10, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Boyang Zhao |
Organization name |
MIT
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Street address |
500 Main Street
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02139 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (1) |
GSE72910 |
Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution |
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Relations |
BioSample |
SAMN04045519 |
SRA |
SRX1220456 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
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