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| Status |
Public on Jun 01, 2016 |
| Title |
SU501-pHSC |
| Sample type |
SRA |
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| Source name |
pHSC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: acute myeloid leukemia, pre-leukemic hematopoietic stem cell
donorid: SU501
sample type: primary human leukemia cell from cryopreserved sample
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from 1,000-100,000 FACS-purified cells using the Qiagen RNeasy Plus Micro Kit
5 ul of total RNA (300 pg – 80 ng) was used as input into the NuGen Ovation V2 cDNA synthesis kit. SPIA-amplified cDNA was sheared using a Covaris S2 sonicator as follows: 10% duty cycle, 5 intensity, 100 cycles/burst, 5 minutes, 120 ul volume. Sheared cDNA was purified and size selected using Ampure XP beads at a 0.9:1 beads:sample ratio. After cleanup, Illumina TruSeq adapters were ligated onto the cDNA using the NEB Next Ultra library prep kit per manufacturer instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using standard input parameters. Aligned reads were filtered for those reads that map uniquely to non-mitochondrial regions.
Duplicate reads (artifacts from amplification) were removed using PICARD MarkDuplicates.
Processed BAM files were analyzed for transcript counts using HTseq against the UCSC refGene transcriptome. Transcript counts were processed using DESeq2, normalizing for both library size and transcript GC content using Conditional Quantile Normalization (Hansen et al., 2012).
Genome_build: hg19
Supplementary_files_format_and_content: Count file is a tab-delimited text file where rows represent unique genes and columns represent unique samples.
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| Submission date |
Oct 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Daniel Buenrostro |
| E-mail(s) |
[email protected]
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| Organization name |
Broad Institute
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE74246 |
Unstranded RNA sequencing data |
| GSE75384 |
Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution |
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| Relations |
| BioSample |
SAMN04202248 |
| SRA |
SRX1363237 |
| 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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