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Sample GSM5814807 Query DataSets for GSM5814807
Status Public on Feb 04, 2022
Title Mpeg Ctrl_rep1
Sample type SRA
 
Source name macrophage
Organism Danio rerio
Characteristics age: 3dpf
batch: 1
genotype: wild type
cell type: macrophage
cell type id: CL:0000235
Treatment protocol Zebrafish larvae were microinjected into one cell stage embryos and screened 3 days post fertilization for transgene expression. Microinjections for TRAP-RNA-sequencing included either control pTol2-krt4-RFP-HRas or oncogenic pTol2-krt4-RFP-HRasG12V constructs injected with pTol2-krt4-GFP-L10a in wildtype larvae, or into Tg(LyzC:EGFP-L10a) or Tg(mpeg1:EGFP-L10a) larvae for keratinocyte, neutrophil, or macrophage-specific expression profiling, respectively. 
Extracted molecule total RNA
Extraction protocol Larvae were stored at -80°C in minimal residual media. QIAshredder (Quiagen) was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent (Invitrogen).
RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low, library prep was done with the NuGEN Ovation Single Cell RNA-Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane, following manufacturer’s protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description polysomal RNA
Data processing Reads were aligned to the transcriptome using Bowtie v1.1.1
Gene abundances were estimated using RSEM v1.2.20
Genome_build: GRCz10,Ensembl 83 annotation
Supplementary_files_format_and_content: The processed data file for each sample is the gene-level abundance output of RSEM and is a tab-delimited text file
 
Submission date Jan 13, 2022
Last update date Feb 04, 2022
Contact name Colin Dewey
Organization name University of Wisconsin-Madison
Street address 425 Henry Mall, 5420 Genetics/Biotechnology Center
City Madison
ZIP/Postal code 53706
Country USA
 
Platform ID GPL14875
Series (1)
GSE193591 Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation
Relations
BioSample SAMN24918789
SRA SRX13773733

Supplementary file Size Download File type/resource
GSM5814807_B8.genes.results.gz 589.9 Kb (ftp)(http) RESULTS
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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