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Status |
Public on Feb 09, 2022 |
Title |
WT_2558_S2 |
Sample type |
SRA |
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Source name |
colon
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Organism |
Mus musculus |
Characteristics |
sample preparation: inDrop scRNA-seq genotype: WT tissue: colon
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Growth protocol |
primary cells
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Extracted molecule |
total RNA |
Extraction protocol |
Human epithelial cell suspensions were obtained by EDTA chelation and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015. MARIS libraries are generated according to Chen et al., 2021. CEL-Seq linear amplification of using standard structure (single index) (Klein et al., 2015) or TruDrop library structure (dual index) (Southard-Smith et al., 2020) RNA-Seq was performed on Novaseq6000 with a 2 x 150 paired-end kit standard run (for dual index) RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths (for single index)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
single index
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Data processing |
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. NextSeq: Technical read: read1 - 3' end - the oligo barcodes are TruDrop which is positioned exactly as in (Klein et al., 2015) Biological read: read2 -UMI/cell barcode NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al., 2020) Biological read: read2 - 3' end Genome_build: Mouse: GRCm38.85 Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows, filtered
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Submission date |
Feb 07, 2022 |
Last update date |
Feb 10, 2022 |
Contact name |
Ken Lau |
E-mail(s) |
ken.s.lau@vanderbilt.edu
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Phone |
6159366859
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Organization name |
Vanderbilt University
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Department |
Cell and Developmental Biology
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Street address |
2215 Garland Ave. MRBIV10475
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City |
Nashville |
State/province |
TN |
ZIP/Postal code |
37232 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (1) |
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Relations |
BioSample |
SAMN25703478 |
SRA |
SRX14071718 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5866569_WT_2558_S2epi_nonepi.h5ad.gz |
13.3 Mb |
(ftp)(http) |
H5AD |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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