|
| Status |
Public on Jul 07, 2024 |
| Title |
Duo_MC1, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Duodenum
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Duodenum
genotype: Mix background
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly collected tissues or cel lines were dissociated using TrypLE at 37 C and neutralized using serum containing buffer, followed by cold PBS wash (3x). Re-suspended single cells were encapsulated using custom inDrop platform, as mentioned in supplemental method section of the paper.
Library was performed according to modified inDrop protocol using TruSeq methods (inDrop V2, PMID: 32616006). Please check the supplemental method section for further details.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Custom inDrop
|
| Data processing |
The demultiplexing, barcode processing, gene count matrix and aggregation were made by dropEst method (https://github.com/kharchenkolab/dropEst).
Assembly: mm10, hg38
Supplementary files format and content: Tab sepatated value files and matrix files
|
| |
|
| Submission date |
Jun 14, 2023 |
| Last update date |
Jul 07, 2024 |
| Contact name |
Mirazul Islam |
| E-mail(s) |
md.mirazul.islam@vanderbilt.edu
|
| Phone |
8577538729
|
| Organization name |
Vanderbilt University
|
| Department |
Cell and Developmental Biology
|
| Lab |
Ken Lau
|
| Street address |
2213 Garland Ave
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE234946 |
Temporal recording of mammalian development and precancer [rna-seq] |
| GSE235119 |
Temporal recording of mammalian development and precancer |
|
| Relations |
| BioSample |
SAMN35735081 |
| SRA |
SRX20679085 |
