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Sample GSM4322679

Query DataSets for GSM4322679

Status

Public on Apr 17, 2020

Title

single cell from LSK-SLAM-13.22 [LIB021528_GEN00057132_S77_R1]

Sample type

SRA

Source name

Fetal liver (FL)

Organism

Mus musculus

Characteristics

tissue: embryonic tissue
strain: C57BL/6

Extracted molecule

total RNA

Extraction protocol

Embryos were harvested from the uterus and dissected in cold dissecting buffer (Dulbecco’s phosphate buffered saline with 10% fetal bovine serum and antibiotics). Dissected tissues were dissociated in 0.125% collagenase type I (Sigma-Aldrich) and 1 U Dispase (Stemcell Technologies) at 37°C for 30 min. The samples were reduced to single cell suspension by mechanical trituration, washed with dissecting media, and passed through 40mm cell strainer. FACS was used to enrich single cell population of interest
Cells were lysed and single cell libraries prepared by the C1 System using the SMARTer Ultra Low RNA Kit (Clontech) and protocols provided by Fluidigm.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

LIB021528_GEN00057132_S77_R1

Data processing

We only use R1 from the pair-end sequence reads. Sequence reads were trimmed to a final length of 40 bases using Trimming software Cutadapt (Martin, 2011).
Salmon (Patro et al., 2017) was used to quasi-map trimmed reads to the reference transcriptome (ENSEMBL (Zerbino et al., 2018) GRCh38.80), including 6511 non-coding RNAs (scaRNAs, lincRNAs, snRNAs, and snoRNAs), to estimate transcript abundances. The number of reads mapping to the transcriptome ranged from 7.7 to 12.0 million. Read counts per gene were derived by summing the counts per transcript across all transcripts associated with the gene
For quality control measures, 0.1% of reads were randomly sampled from each FASTQ and directly aligned to ENSEMBL GRC Release 80 (ftp://ftp.ensembl.org/pub/release-80/gtf/) reference genomes using HISAT2 (Kim et al., 2015) to determine percentage alignment to H. Sapiens, M. Musculus, S. Cerevisiae, E. Coli, and D. Rerio genomes, as well as overlaps with genomic features (including rRNA, mtRNA, protein-coding regions), ambiguous and non-unique alignments, and unaligned reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: comma delimited files containing metadata and count matrix for all samples

Submission date

Feb 20, 2020

Last update date

Apr 17, 2020

Contact name

Yuqi Tan

Organization name

Johns Hopkins University

Street address

733 North Broadway, MRB 653

City

Baltimore