|
Status |
Public on Oct 01, 2023 |
Title |
AEC17 |
Sample type |
SRA |
|
|
Source name |
mouse embryonic cells
|
Organism |
Mus musculus |
Characteristics |
tissue: aorta-gonads-mesonephros (AGM) cell type: AEC 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 |
SAMN22155564 |
SRA |
SRX12528360 |