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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 30, 2019 |
| Title |
E4.5-5.5_new_Plate1_A09 (scRNA-Seq) |
| Sample type |
SRA |
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| Source name |
Early embryo
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6Babr
developmental stage: E5.5
sample type: single cell
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cells were sorted either manually (E4.5, E5.5) or using flow cytometry (E6.5, E7.5) into 96 well PCR plates containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL (Sigma)). Samples were incubated for 15 minutes at 37°C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at -80°C prior to processing. Poly-A RNA was captured on oligo-dT conjugated to magnetic beads and amplified cDNA was prepared according to the G&T-seq and Smartseq2 protocols. The lysate containing gDNA was purified on AMPureXP beads before bisulfite-seq libraries were prepared according to the scBS-seq protocol.
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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 |
Libraries were sequenced on the Illumina Nextseq 500 platform using the default RTA analysis software.
RNA-seq libraries were aligned to the GRCm38 mouse genome build using HiSat270 (v2.1.0) using options --dta --sp 1000,1000 --no-mixed --no-discordant, yielding a mean of 611,000 aligned reads per cell.
Subsequently, gene expression counts were quantified from the mapped reads using featureCounts with the Ensembl gene annotation (version 87). Only protein-coding genes matching canonical chromosomes were considered. The read counts were log-transformed and size-factor adjusted.
Genome_build: GRCm38
Supplementary_files_format_and_content: A table of genes (rows) x cells (columns). The first column is the ensembl gene ID. RNAseq quantitation file.
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| Submission date |
Oct 23, 2018 |
| Last update date |
Sep 30, 2019 |
| Contact name |
Felix Krueger |
| E-mail(s) |
fkrueger@altoslabs.com
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| Organization name |
Altos Labs
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| Department |
Bioinformatics
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| Street address |
Granta Park
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| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE121650 |
Single-cell RNA-seq of mouse embryos E4.5 to E7.5. First batch. |
| GSE121708 |
Multi-omics profiling of mouse gastrulation at single cell resolution |
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| Relations |
| BioSample |
SAMN10277674 |
| SRA |
SRX4917372 |
| 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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