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| Status |
Public on Dec 14, 2015 |
| Title |
1216 Control (MSCVneo +MSCVpuro) polyA RNA-Seq |
| Sample type |
SRA |
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| Source name |
Mouse bone marrow mononuclear cells
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| Organism |
Mus musculus |
| Characteristics |
strain: B6.SJL (CD45.1)
cell type: bone marrow mononuclear cells
treatment: Control (MSCVneo +MSCVpuro)
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| Extracted molecule |
total RNA |
| Extraction protocol |
25 ng of 5hmC-enriched DNA, or non-enriched sonicated input genomic DNA was end-repaired, adenylated, and ligated to Illumina Genomic DNA Adapters (Genomic DNA adapter oligo mix) according to standard Illumina protocols for ChIP-Seq library construction, maintaining the proper molar ratios of adapter to insert. Adapter-ligated fragments of ~200-350 bp were gel-purified by 2% agarose gel electrophoresis and PCR-amplified for 18 PCR cycles. Libraries were checked for quality and quantified using an Agilent 2100 Bioanalyzer DNA 1000 Chip.
RNA-Seq expression libraries were generated from duplicate samples per genotype using the Illumina TruSeq RNA Sample Preparation Kit v2. Libraries were sequenced using the Illumina HiScan platform. Cluster generation was performed with Illumina TruSeq cluster kit v2-cBot-HS. Single-read 51-bp sequencing was completed with Illumina TruSeq SBS kit v3-HS. Single-read 51-bp sequencing was completed with Illumina TruSeq SBS kit v3-HS.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
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| Data processing |
Illumina Basecalling, CASAVA 1.8.2
FASTQ sequences were aligned to NCBIv1/mm9 with Bowtie v0.17.2 retaining unique non-duplicate matches to the genome, with no more than 3 mismatches in the first 30 bases
Enriched regions derived from MACS v1.4, --bw=200 -g 1.87e9, using genotype matched input controls
RNA-Seq reads were aligned using tophat-1.4.1 and RPKM expression values were extracted using cufflinks-1.3.0 using RefSeq gene models.
Genome_build: mm9
Supplementary_files_format_and_content: BED format, containing regions of enrichment and RPKM expression values
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| Submission date |
Dec 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Keith E Szulwach |
| E-mail(s) |
kszulwa@emory.edu
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| Phone |
404-712-0796
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| Organization name |
Emory University
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| Department |
Human Genetics
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| Lab |
Jin Lab
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| Street address |
615 Michael Street, Whitehead Suite 301
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL16173 |
| Series (1) |
| GSE42990 |
Tet1 plays an essential oncogenic role in MLL-rearranged leukemia |
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| Relations |
| SRA |
SRX211358 |
| BioSample |
SAMN01831627 |
| 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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