|
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 |