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| Status |
Public on Jan 23, 2019 |
| Title |
CD3 |
| Sample type |
SRA |
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| Source name |
cord blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: cord blood
cell type: leukocytes
developmental stage: newborn
condition: cesarean delivery
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| Treatment protocol |
The cord blood of newborns was collected into a sterilized heparin anticoagulant tube, and then centrifuged for the separation of leukocytes.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol reagent
The purified mRNA was fragmented (200bp-300bp) using divalent cations under elevated temperature. These short fragments were copied into the first-strand cDNA using random hexamer primers and reverse transcriptase (Invitrogen, Carlsbad, CA, USA). Second-strand cDNA was synthesized with adding of DNA Polymerase I and RNase H. The products were then enriched by PCR amplification for 15 cycles, separated by Certified Low Range Ultra Agarose (Bio-Rad, USA) gel electrophoresis, and further analyzed for quality on an Agilent 2100 Bioanalyzer (Agilent technologies). The amplicons in the sizes of 300–400 bps were collected and purified.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
The raw reads were cleaned by removing adapter sequences and low quality sequences (reads with over 5% undetermined base pairs‘N’). Then, the high quality reads were assembled using Trinity and further mapped to the human genome (hg19) using TopHat v2.0.11 with the default parameters.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample
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| Submission date |
Jan 22, 2019 |
| Last update date |
Jan 26, 2019 |
| Contact name |
Yongjie Liu |
| E-mail(s) |
liuyuan198808@163.com
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| Organization name |
Xinhua Hospital, Shanghai Jiao Tong University School of Medicine
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| Street address |
1665 kongjiang road
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE125421 |
A comprehensive gene expression analysis identifies novel immune signatures in cesarean-born infants |
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| Relations |
| BioSample |
SAMN10787595 |
| SRA |
SRX5275795 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3573695_Sample_S3_20160723_S3_L004.count.txt.gz |
257.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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