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| Status |
Public on Oct 05, 2015 |
| Title |
BAP1 KO GMP 3 |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: granulocyte macrophage progenitors (GMP)
genotype: MX1+ Cre Bap1 f/f
age: 65 days (pIpC at 42 days)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow was extracted and red cell lysed, cells were stained for GMP markers (Lineage-c-Kit+Sca1-CD34+Fcϒ), and sorted using a FACS Aria. RNA was harvested using Trizol reagent. Smart Clontech RNA Kit (Cat# 635001) was used with 20 ng RNA for library construction.
10ng of high quality total RNA was amplified using the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech Laboratory, cat# 634940) according to manufacturer instructions. Amplified material underwent whole transcriptome library preparation according to the Ion Total RNA-Seq Kit v2 protocol (Life Technologies), with 16 cycles of PCR.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
BAM converted back to FASTQ using PICARD Sam2Fastq.
Reads mapped to mm9 (junctions from ENSEMBL, Mus_musculus.NCBIM37.67) using STAR RNA-seq aligner, using read overhang of 49
Unmapped reads were mapped to mm9 using BWA MEM (version 0.7.5a).
The two mapped BAM files were merged and sorted.
Gene level counts computed using htseq-count (options -s y -m intersection-strict).
Differential expression analysis was performed with the R Bioconductor DESeq2 package using default parameters.
Genome_build: mm9, ENSEMBL Mus_musculus.NCBIM37.67
Supplementary_files_format_and_content: Normalized count tables provided as computed by DESeq2.
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| Submission date |
Sep 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Barbara Spitzer |
| E-mail(s) |
spitzerb@mskcc.org
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| Organization name |
Memorial Sloan Kettering Cancer Center
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| Lab |
Levine Lab
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| Street address |
411 E 67th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL18635 |
| Series (1) |
| GSE61577 |
Bap1 loss results in EZH2 dependent transformation |
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| Relations |
| BioSample |
SAMN04113190 |
| SRA |
SRX1288076 |
| 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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