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Status |
Public on Oct 13, 2017 |
Title |
Liver_ALGS4 |
Sample type |
SRA |
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Source name |
Alagille syndrome_liver needle biopsy
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Organism |
Homo sapiens |
Characteristics |
subject status: Alagille syndrome tissue: Liver
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Extracted molecule |
polyA RNA |
Extraction protocol |
RNA extraction of homogenized human liver biopsies was performed using Direct-zol™ RNA MiniPrep (cat. no. R2050, Zymo Research), including on-column DNase I digestion (cat. no. E1009, Zymo Research). cDNA libraries for all samples were created using the TruSeq® RNA Sample Prep Kit v2–48, Set A (cat. no. RS-122-2001, Illumina®,) as per the TruSeq® RNA Sample Preparation v2 Guide, Low-Throughput Protocol.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
RPKM L6_AlagillePatient5
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Data processing |
Reads were aligned using STAR to genomes mm10 and hg19 Reads were separated for different species using S^3 (https://github.com/danielramskold/S3_species-specific_sequencing) with default settings (-Ms 1 -Mu 1 -D 2) Unique reads were selected using mapping quality threshold 255 Gene expression values were calculated using rpkmforgenes.py (see link above) with options -rmnameoverlap -bothendsceil and using RefSeq annotation from 1 July 2014 MicroRNAs and snoRNAs were removed RPKM values were TMM normalized Genome_build: hg19 Supplementary_files_format_and_content: Tab-delimited text of normalised expression values and read counts
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Submission date |
Oct 12, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Urban Lendahl |
Organization name |
Karolinska Insttitutet
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Street address |
Von Eulers vag 3
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City |
Stockholm |
ZIP/Postal code |
17177 |
Country |
Sweden |
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Platform ID |
GPL11154 |
Series (2) |
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Relations |
BioSample |
SAMN07776820 |
SRA |
SRX3275358 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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