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| Status |
Public on Jun 23, 2022 |
| Title |
liver, pediatric normal, 6 |
| Sample type |
SRA |
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| Source name |
liver explant tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: liver explant tissue
disease state: normal
age: 4yo
gender: male
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from frozen liver samples using TRIZOL reagent (Ambion by Life Technologies, Carlsbad, CA), and cDNA was synthesized with the qScript cDNA synthesis kit (Quantabio, Beverly, MD)
The stranded mRNA-seq was conducted in the Northwestern University NUSeq Core Facility. Briefly, total RNA examples were checked for quality using RINs generated from Agilent Bioanalyzer 2100. RNA quantity was determined with Qubit fluorometer. The Illumina Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries from 100 ng of high-quality RNA samples (RIN>7). All 34 samples met QC standards and were used for the study. The kit procedure was performed without modifications. This procedure includes mRNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
9609
4yo male
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| Data processing |
Reads were trimmed using trimgalore
trimmed reads were aligned using star
aligned reads were counted using htseq-count
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
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| Submission date |
Jun 17, 2022 |
| Last update date |
Jun 24, 2022 |
| Contact name |
Alyssa Kriegermeier |
| E-mail(s) |
akriegermeier@luriechildrens.org
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| Phone |
8474146125
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| Organization name |
Ann and Robert H. Lurie Children's Hospital of Chicago
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| Department |
GI/Hepatology/Nutrition
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| Street address |
225 E. Chicago
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE206364 |
The IRE1α/XBP1 pathway expression is impaired in pediatric cholestatic liver disease explants |
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| Relations |
| BioSample |
SAMN29178711 |
| SRA |
SRX15781789 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6252631_S9609.txt.gz |
197.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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