|
| Status |
Public on Mar 17, 2022 |
| Title |
AB89 |
| Sample type |
SRA |
| |
|
| Source name |
ESC differentiation
|
| Organism |
Mus musculus |
| Characteristics |
Stage: Org_2
cell type: in vitro ESC-derived endoderm organoids
|
| 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)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
read2 concatenated to R1 header separated to plate barcode - cell barcode - UMI
|
| 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
Supplementary_files_format_and_content: [metadata_s.txt] Meta data file associating each single cell with its amplification batch and index sorting readouts
|
| |
|
| Submission date |
Sep 21, 2021 |
| Last update date |
Mar 17, 2022 |
| Contact name |
Josh M Brickman |
| E-mail(s) |
joshua.brickman@sund.ku.dk
|
| Organization name |
Copenhagen University
|
| Department |
reNEW
|
| Lab |
Brickman
|
| Street address |
3B Blegdamsvej
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE164464 |
Identification of the central intermediate in the extra-embryonic to embryonic endoderm transition through single cell transcriptomics |
|
| Relations |
| BioSample |
SAMN21536506 |
| SRA |
SRX12287245 |
