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Sample GSM2310406 Query DataSets for GSM2310406
Status Public on Oct 28, 2016
Title MC1
Sample type SRA
 
Source name Bone marrow derived macrophage precursors
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Bone marrow
condition: 6 days M-CSF treatment
dna content: 2c
Treatment protocol Cells were re-plated in OptiMEM medium and stimulated with M-CSF (50ng/ml) ('control') or M-CSF (50ng/ml) and (FSL-1 20ng/ml) for 6 days.
Growth protocol Bone marrow cells were flushed from the femurs of mice and cultured with murine M-CSF (20 ng/ml) on petri dishes in DMEM supplemented with 10% FBS for 4-5 days. The adherent cell population (referred to as ‘macrophage precursors’) was then recovered and plated at 2x104 cells/ml in OptiMEM medium containing 10% FBS and 50ng/ml M-CSF.
Extracted molecule total RNA
Extraction protocol Hoechst staining was performed on control and FSL-1 treated cells to quantify the DNA content and single cells were FACS-sorted using BD Influx in 384-well plates.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description library of 96 2c M-CSF treated cells
Data processing For image aquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The 65bp right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The 25bp left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for quantification.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
 
Submission date Sep 14, 2016
Last update date May 15, 2019
Contact name Sagar -
E-mail(s) sagar@uniklinik-freiburg.de
Organization name University Medical Center Freiburg
Department Department of Internal Medicine II
Lab Sagar
Street address Hugstetter Straße 55
City Freiburg
ZIP/Postal code 79106
Country Germany
 
Platform ID GPL17021
Series (1)
GSE86929 Single cell RNA sequencing analysis of bacterial lipoprotein-induced polyploid macrophages.
Relations
BioSample SAMN05772510
SRA SRX2163664

Supplementary file Size Download File type/resource
GSM2310406_MC1.coutt.csv.gz 321.8 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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