|
| Status |
Public on Oct 01, 2023 |
| Title |
HEC21 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: aorta-gonads-mesonephros (AGM)
cell type: Hematopoietic stem cells
developmental stage: E10.0
|
| Treatment protocol |
FACS-sorted cells were kept on ice until lysed and reverse transcribed.
|
| Growth protocol |
Wildtype AECs and HECs were sorted from the E10 embryonic AGM region of C57 mice.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Morphologically deformed cells were discarded. Living single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette; 0.05 μl of 1:200,000 dilution of External RNA Controls Consortium (ERCC) RNA spike-in Mix1 (Ambion) was added to lysis buffer per reaction.
The cDNA fragments were end-repaired and added dA-tailed using Ultra II End Prep module and then tethered to 1D adaptor by using Quick Ligation Module. After that, each cDNA library was loaded into 1 FLOPRO002 flow cell and sequenced on PromethION.Beta.
PolyA enriched single-cell Nanopore Sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
Guppy (V3.5.2) software used for basecalling.
Sequenced reads were firstly processed with nanopack, then mapped to GENCODE (vM22) mouse genome (mm10) with minimap2 (v2.18-r1015) with default parameters
Isofrorm-level expression was quantified as counts with Salmon (version 1.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPT10K at isoform level.
|
| |
|
| Submission date |
Oct 08, 2021 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Jia Yu |
| E-mail(s) |
j-yu@ibms.pumc.edu.cn
|
| Organization name |
Peking Union Medical College
|
| Street address |
Dong Dan San Tiao 5, Dongcheng District
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL26624 |
| Series (2) |
| GSE185554 |
Single-cell Architecture and Functional Requirement of Alternative Splicing during Hematopoietic Stem Cell Emergence [RNA-Seq] |
| GSE185555 |
Single-cell Architecture and Functional Requirement of Alternative Splicing during Hematopoietic Stem Cell Emergence |
|
| Relations |
| BioSample |
SAMN22155594 |
| SRA |
SRX12528391 |
