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Sample GSM7043044 Query DataSets for GSM7043044
Status Public on May 09, 2023
Title K49A-3_2-cell
Sample type SRA
 
Source name embryo
Organism Mus musculus
Characteristics cell type: 2-cell
tissue: embryo
strain: C57BL6
age: 26 - 28 hours post fertilization
Extracted molecule total RNA
Extraction protocol Two-cell embryos were collected between 26 and 28 hours post fertilization. Each embryo was immediately placed into a single well of a plexWell Rapid Single Cell plate (SmartSeq Platform), which was then frozen until sample prep.
Libraries were generated from 2 cell embryos using Smart Seq2 platform.
Single-embryo RNA sequencing using NovaSeq 6000 Illumina platform
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Smart-seq2
Sample_5056-LM-21
Data processing The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011).
Alignment options followed ENCODE standards for RNA-seq (Dobin).
Assembly: mm10
Supplementary files format and content: Tab-delimited gene expression matrix
 
Submission date Feb 14, 2023
Last update date May 09, 2023
Contact name Qianyi Ma
E-mail(s) qzm100@gmail.com
Organization name University of Michigan
Department Human Genetics
Street address 1141 E Catherine St
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL24247
Series (2)
GSE225270 Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse Protamine 1 [scRNA-Seq]
GSE225271 Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse Protamine 1
Relations
BioSample SAMN33285529
SRA SRX19364286

Supplementary file Size Download File type/resource
GSM7043044_Sample_5056-LM-21.count.txt.gz 106.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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