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Sample GSM5618248 Query DataSets for GSM5618248
Status Public on Oct 01, 2023
Title AEC16
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 SAMN22155563
SRA SRX12528359

Supplementary file Size Download File type/resource
GSM5618248_AEC16.RPT10K.tsv.gz 245.0 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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