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| Status |
Public on Jun 01, 2016 |
| Title |
singles-SU070-LSC-3 |
| Sample type |
SRA |
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| Source name |
LSC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: acute myeloid leukemia, leukmeia stem cell
donor id: SU070
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers (Supplementary Table 1) in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL. The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
library strategy: scATAC-seq
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| Data processing |
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
Genome_build: hg19
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| Submission date |
Oct 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Daniel Buenrostro |
| E-mail(s) |
jdbuenrostro@gmail.com
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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) |
| GSE74310 |
Single-cell chromatin accessibility data using scATAC-seq |
| GSE75384 |
Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution |
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| Relations |
| Reanalyzed by |
GSE99172 |
| BioSample |
SAMN04210971 |
| SRA |
SRX1371558 |
| 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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