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| Status |
Public on Dec 18, 2020 |
| Title |
sc_AC1_266_sample_0003 |
| Sample type |
SRA |
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| Source name |
Tissue
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| Organism |
Xenopus tropicalis |
| Characteristics |
cell line: none
Stage: stage10 .5 (Gastrula)
antibody: none
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| Extracted molecule |
total RNA |
| Extraction protocol |
Dissected embryo explants were dissociated into single cells using Ca2+ and Mg2+ free media (Sive, Grainger, & Harland, 2007). 200 cells were picked for performing single-cell RNA-seq using the modified version of Tang et al protocol (Tang et al., 2008).
Amplified cDNA was purified with XP beads and the Zymo purification kit respectively and its concentration measured with Qubit® 2.0 Fluorometer (Q32866, Life Technologies). The quality of the amplified cDNA and distribution of DNA fragment size were assessed by Agilent 2100 Bioanalyzer (Agilent Technologies) with the High Sensitivity DNA Kit (5067-4626, Agilent). The sequencing libraries were prepared using the KAPA Hyper Pre Kit (KR0961 – v6.17, Kapa Biosystems). The concentrations of the fragments with the approximate indexed adapters were quantified by KAPA library quantification.
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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 |
samplename_reads.tab file is generated with STAR 2.5.0 with the option of --quantMode GeneCounts
Genome_build: xt9
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| Submission date |
Feb 20, 2020 |
| Last update date |
Dec 18, 2020 |
| Contact name |
Ann Rose Bright |
| Organization name |
RIMLS
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| Department |
Department of Molecular Biology
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| Street address |
Geert Grooteplein Zuid 30
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| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
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| Platform ID |
GPL24884 |
| Series (1) |
| GSE145619 |
Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates |
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| Relations |
| BioSample |
SAMN14145624 |
| SRA |
SRX7759424 |
| 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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