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Sample GSM2322019 Query DataSets for GSM2322019
Status Public on Aug 01, 2017
Title Mono_day 10 batch1
Sample type SRA
Source name CD34-positive HSC induced to monocytic differentiation for 10 days
Organism Homo sapiens
Characteristics developmental stage: Monocytic middle stage
tissue: hematopoietic systerm
batch: batch1
Treatment protocol G-CSF and M-CSF
Growth protocol IMDM+FBS+IL-3
Extracted molecule total RNA
Extraction protocol Trizol reagent
polyA-enriched RNA
illumina RNA-seq library
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description CD34-positive HSC induced to monocytic differentiation for 10 days
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trim Galore v0.3.7 with parameters -q 25 --stringency 5 --length 50 --paired --phred33, and filtered for low-quality sequence, then mapped to hg38 whole genome of GENCODE v25 using tophat v2.1.0 with parameters -p 14 --splice-mismatches 1 --segment-mismatches 2 --mate-inner-dist 50 --mate-std-dev 20 --library-type fr-unstranded
Non-normalized raw counts were calculated using featureCounts v1.5.0 with parameters -T 7 --primary. In short, exons from all isoforms of a gene were merged to create one meta-transcript. Fragments Per Kilobase of exon model per Million (FPKM) mapped reads were calculated using cufflinks v2.2.1 with parameters -p 10 -u --library-type fr-unstranded -G gencode.v24.annotation.gtf.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include non-normalized raw counts and FPKM values for each Sample.
Submission date Sep 19, 2016
Last update date May 15, 2019
Contact name Jia Yu
Organization name Peking Union Medical College
Street address Dong Dan San Tiao 5, Dongcheng District
City Beijing
ZIP/Postal code 100005
Country China
Platform ID GPL21290
Series (1)
GSE87088 KSRP specifies monocytic and granulocytic differentiation through regulating miR-129 biogenesis and RUNX1 expression
BioSample SAMN05788812
SRA SRX2175638

Supplementary file Size Download File type/resource
GSM2322019_M10d1.genes.fpkm_tracking.gz 1.6 Mb (ftp)(http) FPKM_TRACKING
GSM2322019_M10d1.raw.counts.txt.gz 3.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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