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Sample GSM2782250

Query DataSets for GSM2782250

Status

Public on Apr 27, 2018

Title

RNA-seq, S2-AML2 (478)

Sample type

SRA

Source name

xenografted leukemic (AML) mouse bone marrow cells

Organism

Homo sapiens

Characteristics

injected cells: t(9;11) chromosome rearranged human CD34+ cells
host strain: NOD.Cg-PrkdcscidIL2rgtm1Wjl/SzJ (NSG)
tissue: bone marrow

Treatment protocol

CD34+ human umbilical cord blood cells were nucleofected with TALENs tageting MLL and AF9. 100% t(9;11) chromosomal rearranged, and MLL-AF9 fusion, cells after in vitro culture for 98 days were transplated into sublethally irradiated NSG mice. After signs of illness, mice were sacrificed and bone marow cells as well as the injected cells were harvested for RNA extraction. Bone marrow cells from sick mice were transplanted into secondary NSG mice recipient. Secondary transplated mice were sacrificed when they were sick and bone marrow cells were harvested for RNA extraction.

Growth protocol

t(9;11) chromosome rearranged human CD34+ cells were transplanted into NSG mice. Sick mice were sacrificed. Median latency was 48 weeks.

Extracted molecule

total RNA

Extraction protocol

RNA was purified from leukemic mouse bone marrow and cultured cells using Trizol (Invitrogen) followed by RNeasy kit (Qiagen) as manufacturer’s instructions.
Single-ended 50 bp reads (59 million per sample on average) were generated using a BGISEQ-500 platform (BGI America Co., Cambridge, MA).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

BGISEQ-500

Description

RNA-seq, S2-AML2 (478)

Data processing

RNA-seq was performed using a BGISEQ-500 platform and the raw reads were filtered for adaptor sequence, masked for low-complexity or low-quality sequence.
Clean reads were mapped to hg19 using HISAT/Bowtie2 tool.
Gene expression level was qantified by RSEM and FPKM was calculated.
Somatic SNP/Indel calling and annotation were performed using VarScan 2 followed by VEP in DNAnexus cloud platform (dnanexus.com). Human genome reference GRCh37/hg19, minimum coverage of 50, and p-value threshold of 0.05 were used. SNV/Indels were manually confirmed using IGV. ClinVar database was used to search pathogenic mutation and GRCm38.p4 mouse genome reference used to filter out mouse sequence.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

Submission date

Sep 13, 2017

Last update date

May 15, 2019

Contact name

Johan Jeong

E-mail(s)

[email protected]

Phone

6507235340

Organization name

Stanford University