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Sample GSM4255677 Query DataSets for GSM4255677
Status Public on Jan 08, 2020
Title MON 1208
Sample type SRA
 
Source name peripheral blood
Organism Mus musculus
Characteristics cell type: monocytes (Gr-1+Mac-1+)
strain: C57BL6
developmental stage: adult
Extracted molecule total RNA
Extraction protocol After Ficoll separation of peripheral blood, monocytes (Gr-1+Mac-1+) were sorted from the mononuclear fraction.
Total RNA was extracted using TRIzol and the Ambion PureLink RNA Mini Kit (Life Technologies, cat# 12183018), treated with DNase to remove genomic DNA using the DNAfree Kit (Life Technologies, cat# AM1906).
Sequencing libraries were constructed from 100 ng of DNase-treated, total RNA using the ScriptSeqv2 Complete Kit (Illumina cat# BHMR1224). The RNA depleted for rRNA using the Ribo-Zero removal reagents and fragmented. First strand cDNA was then synthesized using a 5’ tagged random hexamer and reverse transcription, followed by annealing of a 5’ tagged, 3’-end blocked terminal-tagged oligo and second strand synthesis. The Di-tagged cDNA fragments were purified, barcoded, and PCR-amplified for 15 cycles.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description monocyte
Data processing Illumina's bcl2fastq2 to generate fastq files
The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/). In brief, reads were mapped to the mouse genome using STAR, followed by RSEM for gene quantifications using Gencode vM4 genes.
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from STAR
Supplementary_files_format_and_content: tsv, expression levels from RSEM
 
Submission date Jan 07, 2020
Last update date Jan 08, 2020
Contact name Ross Hardison
E-mail(s) rch8@psu.edu
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL19057
Series (2)
GSE143261 An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [RNA-seq]
GSE143271 An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
Relations
BioSample SAMN13750527
SRA SRX7517165

Supplementary file Size Download File type/resource
GSM4255677_1208.tsv.gz 2.3 Mb (ftp)(http) TSV
GSM4255677_1208minus.mm10.bw 70.9 Mb (ftp)(http) BW
GSM4255677_1208plus.mm10.bw 70.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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