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| Status |
Public on Jul 17, 2015 |
| Title |
Q119 |
| Sample type |
SRA |
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| Source name |
Fetal cord blood, control
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| Organism |
Homo sapiens |
| Characteristics |
cell type: cord blood mononuclear cells
developmental stage: 18-22 weeks of gestation
karyotype: 46,XX and 46,XY
sample type: pool of 3 samples
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cord blood mononuclear cells (CBMCs) were separated by a Ficoll-Paque. Total RNA was harvested using Trizol reagent. The 18-30nt small RNA population was isolated by separating 10 μg of total RNA using denaturing polyacrylamide gel electrophoresis (PAGE). The Illumina Small RNA Sample Prep Kit (Cat# FC-102-1009) was used to construct the sequencing libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Small RNA
Control group
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| Data processing |
Illumina Casava 1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Homo sapiens whole genome using SOAP(2.0) with parameters soap -v 0 -r 2 -s 7 -p 7 -a clean.fa -d ref_genome.fa -o match_genome.soap
The mapped sequences were aligned against miRBase17.0, Rfam 10.0 (http://rfam.sanger.ac.uk/), piRNABank (NCBI) and the human genes UCSC annotation hg19 (http://genome.ucsc.edu/). Overlapping annotation sequences from these data were classified as miRNA, tRNA, rRNA, mRNA, snoRNA, snRNA, piRNA or other non-coding RNAs.
Before expression analysis of known miRNAs, the miRNA expression level was normalized by calculating its transcripts parts per million (TPM). The total clone count is the sum of the frequencies of all unique sequences remaining after filtering.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values or identified novel miRNAs for each Sample.
Supplementary_files_format_and_content: *txt: abundance measurements
Supplementary_files_format_and_content: *nov.txt: identified novel miRNAs
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| Submission date |
Jul 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wuxian Li |
| E-mail(s) |
liwuxiancqmu@yahoo.cn
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| Phone |
18664568186
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| Fax |
+86 755-25626750
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| Organization name |
the Second Clinical Medical College of Jinan University
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| Street address |
1017, North road, Dongmen
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518020 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE39436 |
MicroRNA profiling and discovery by deep sequencing cord blood from Down syndrome fetuses |
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| Relations |
| SRA |
SRX160493 |
| BioSample |
SAMN01090684 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM968721_Q119-nov.txt.gz |
17.5 Kb |
(ftp)(http) |
TXT |
| GSM968721_Q119.txt.gz |
3.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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