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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 17, 2022 |
| Title |
AB57 |
| Sample type |
SRA |
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| Source name |
Foxa2-Venus mouse embryos
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| Organism |
Mus musculus |
| Characteristics |
developmental stage: E8.5
cell type: Foxa2-Venus positive populations - notochord, gut, floor plate, visceral endoderm
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Embryos were dissociated with Accutase (Sigma) into singlet cells immediately after collection, the in vitro differentiated cells were dissociated by 0.1% trypsin.
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation
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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 |
library strategy: MARS-seq
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: [AB*.txt] single cell expression matrix include mRNA molecule count values for each Sample
[metadata_s.txt] Meta data file associating each single cell with its amplification batch and index sorting readouts
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| Submission date |
Jan 08, 2021 |
| Last update date |
Mar 17, 2022 |
| Contact name |
Josh M Brickman |
| E-mail(s) |
joshua.brickman@sund.ku.dk
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| Organization name |
Copenhagen University
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| Department |
reNEW
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| Lab |
Brickman
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| Street address |
3B Blegdamsvej
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| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE164464 |
Identification of the central intermediate in the extra-embryonic to embryonic endoderm transition through single cell transcriptomics |
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| Relations |
| BioSample |
SAMN17261304 |
| SRA |
SRX9807905 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5011389_AB87.txt.gz |
543.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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