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Sample GSM2322013 Query DataSets for GSM2322013
Status Public on Aug 01, 2017
Title Gran_day 10 batch1
Sample type SRA
 
Source name CD34-positive HSC induced to granulocytic differentiation for 10 days
Organism Homo sapiens
Characteristics developmental stage: Granulocytic 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 granulocytic 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
E-mail(s) j-yu@ibms.pumc.edu.cn
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
Relations
BioSample SAMN05788808
SRA SRX2175632

Supplementary file Size Download File type/resource
GSM2322013_G10d1.genes.fpkm_tracking.gz 1.6 Mb (ftp)(http) FPKM_TRACKING
GSM2322013_G10d1.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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