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| Status |
Public on Feb 28, 2020 |
| Title |
19355 RNA-Seq |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
individual: 19355
chromosomes: XXY
tissue: blood
cell type: primary lymphocytes
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| Extracted molecule |
total RNA |
| Extraction protocol |
Lymphocytes were isolated from whole blood samples by centrifugation after dilution with PBS and underlaying Sigma Histopaque-1077 to the bottom. Genomic DNA and total RNA were extracted simultaneously from lymphocytes using QIAGEN's AllPrep DNA/RNA Mini Kit.
Illumina’s TruSeq Stranded RNA with Ribo-Zero (Human) for ribo-depletion kit was used to construct strand specific libraries for each sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
RNA-Seq data: Cutadapt (version 1.8.1) was used to trim Illumina TruSeq adapters and low-quality ends from the raw reads. Bowtie2 (version 2.3.1) was used to align the trimmed reads to the GENCODE comprehensive gene annotation (release 23, hg38) and RSEM (version 1.2.30) was used to quantify gene expression in a strand-specific manner by setting parameter “--forward-prob 0”. DESeq2 (version 1.12.4) was used to perform differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: [RNA-Seq data] gene id, transcript id, length, effective_length, expected count, TPM, FPKM
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| Submission date |
Feb 18, 2019 |
| Last update date |
Feb 28, 2020 |
| Contact name |
Xianglong Zhang |
| Organization name |
Amgen Inc.
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| Department |
Department of Cardiometabolic Disorders
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| Street address |
One Amgen Center Dr.
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| City |
Thousand Oaks |
| State/province |
CA |
| ZIP/Postal code |
91320 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE126712 |
Comparative and integrated functional genomics analysis of Klinefelter and Turner syndromes reveals network-wide effects of the sex chromosome dosage changes |
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| Relations |
| BioSample |
SAMN10962737 |
| SRA |
SRX5388852 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3611728_19355.genes.results.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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