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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 27, 2018 |
| Title |
RNA-seq, S1-AML4 (474) |
| Sample type |
SRA |
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| Source name |
xenografted leukemic (AML) mouse bone marrow cells
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| Organism |
Homo sapiens |
| Characteristics |
injected cells: t(9;11) chromosome rearranged human CD34+ cells
host strain: NOD.Cg-PrkdcscidIL2rgtm1Wjl/SzJ (NSG)
tissue: bone marrow
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| 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.
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| Growth protocol |
t(9;11) chromosome rearranged human CD34+ cells were transplanted into NSG mice. Sick mice were sacrificed. Median latency was 48 weeks.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Description |
RNA-seq, S1-AML4 (474)
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| 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 ...
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| Submission date |
Sep 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Johan Jeong |
| E-mail(s) |
jeong401@gmail.com
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| Phone |
6507235340
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| Organization name |
Stanford University
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| Department |
Pathology
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| Lab |
Cleary Lab
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| Street address |
Rm.G2035, 265 Campus Dr.
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE103811 |
MLL leukemia induction by t(9;11) chromosomal translocation in human hematopoietic stem cells using genome editing |
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| Relations |
| BioSample |
SAMN07638363 |
| SRA |
SRX3182212 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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