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SRX2281605: GSM2364216: C10-18h; Mus musculus; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 1.2M spots, 172.3M bases, 81.1Mb downloads

Submitted by: NCBI (GEO)
Study: Integrative analysis of single-cell ATAC-seq and RNA-seq using Self-Organizing Maps [scRNA-Seq]
show Abstracthide Abstract
We have developed a computational approach that uses self-organizing maps for integrative genomic analysis. We utilize this approach to identify the single-cell chromatin and transcriptomic profiles during mouse pre-B cell differentiation. Overall design: We use the C1 Fluidigm system to profile gene expression and chromatin accessibility in single-cells during pre-B cell differentiation.
Sample: C10-18h
SAMN05951486 • SRS1766678 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Single cells were isolated using the Fluidigm C1 System. Single cell C1 runs were completed using the smallest IFC (5-10 um) based on the estimated size of B3 cells. Briefly, cells were collected for 0,2,6,12,18 and 24 hour time-points at a concentration of 400 cells/μl in a total of 50 μl. To optimize cell capture rates on the C1, buoyancy estimates were optimized prior to each run. Each individual C1 capture site was visually inspected to ensure single-cell capture and cell viability. After visualization, the IFC was loaded with Clontech SMARTer kit lysis, RT, and PCR amplification reagents. cDNA was normalized across all libraries from 0.1-0.3 ng/μl and libraries were constructed using Illumina’s Nextera XT library prep kit per Fluidigm’s protocol. Constructed libraries were multiplexed and purified using AMPure beads. The final multiplexed single-cell library was analyzed on an Agilent 2100 Bioanalyzer for fragment distribution and quantified using Kapa Biosystem’s universal library quantification kit. The library was normalized to 2 nM and sequenced as 75bp paired-end dual indexed reads using Illumina’s NextSeq 500 system at a depth of ~1.0-2.0 million reads per library.
Experiment attributes:
GEO Accession: GSM2364216
Links:
Runs: 1 run, 1.2M spots, 172.3M bases, 81.1Mb
Run# of Spots# of BasesSizePublished
SRR44782431,172,934172.3M81.1Mb2019-02-15

ID:
3345134

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