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Sample GSM1599131 Query DataSets for GSM1599131
Status Public on Feb 01, 2016
Title CD4_0y_3 small RNA-seq
Sample type SRA
 
Source name CD4+ T cell
Organism Homo sapiens
Characteristics age: Newborn
cell type: CD4+ T cell
Treatment protocol Peripheral blood mononuclear cells (PBMCs) were isolated from the pooled blood samples using density gradient centrifugation and CD4+ T cells were isolated by positive selection using CD4 beads
Growth protocol All subjects acceded to a basic physical examination and chest X-rays when the blood samples were harvested. Primary criteria for inclusion in the study were the absence of overt systemic diseases, such as cancer, cardiovascular events, autoimmune diseases or dementia. Furthermore, the long-lived subjects had to be able to perform some daily living activities, and even simple farm work and answer a health and family history questionnaire.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Qiagen RNeasy RNA mini kit. Library preparation following "TruSeq RNA Sample Preparation Guide".
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer IIx
 
Data processing Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the Ensembl-RNA reference sequence 38 using FanSe2 with parameters: -L110 -E7 -U0 -S10; miRNA-seq reads were aligned to the mirBase 19 using bowtie with parameters: -N 0; MeDIP-seq reads were aligned to human Hg18 genome using SOAPaligner version 2.21 with parameters -s 34 -v 2 -g 0 -r 1 -M 4.
Gene and miRNA abundance measurements were generationed and normalized using DESeq version 1 ; The normalized standard were condition-dependent per-gene value (CDPV); DMR measurements were generationed and normalized with SOAPaligner
Differential gene and miRNA expression were analysed using DEGseq function package in R program version 2.15.3; Differential DMR were analysed using MACS version 1.4.0
Genome_build: UCSC human Hg18
Supplementary_files_format_and_content: tab-delimited text files include normalized CDPV, TMP or DMR values and raw fragment counts for each Sample
 
Submission date Feb 02, 2015
Last update date May 15, 2019
Contact name Hanqi Yin
E-mail(s) yhqjndx@163.com
Phone 86-18926104647
Organization name shanghai biochip corporation
Street address libing road 151
City Shanghai
State/province Shanghai
ZIP/Postal code 86-21
Country China
 
Platform ID GPL10999
Series (1)
GSE65515 Distinct epigenomes in CD4+ T cells of newborns, middle-ages and centenarians.
Relations
BioSample SAMN03324189
SRA SRX863128

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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