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Sample GSM5965591 Query DataSets for GSM5965591
Status Public on Apr 06, 2023
Title Liver tissue sample [129RD]
Sample type SRA
 
Source name Liver tissue
Organism Homo sapiens
Characteristics cell type: Ductular reaction cells
Treatment protocol N/A
Growth protocol Liver cell populations (Hepatocytes, hepatobiliary cells and ductular reaction cells) were isolated by laser capture microdissection as previously described in Aguilar-Bravo et al, Hepatology 2019
Extracted molecule total RNA
Extraction protocol RNA-Seq analysis was performed using 1-10ng of RNA per sample. For each sample, libraries were created using the AmpliSeq Transcriptome Human Gene Expression Kit (ThermoFisher Scientific, ref. A26325) and the User Guide MAN0010743 (Revision C.0) with minor modifications.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description Ductular reaction cells: 129RD
Data processing FASTQ files were trimmed with Quality Score method
Torrent Suite Software v 5.2 was used for basecalling, alignment, and mapping validated reads to HG19 transcriptome and AmpliSeq specific bed files.
Assembly: Genome_build: hg19
Supplementary files format and content: read counts RNA-seq
 
Submission date Mar 22, 2022
Last update date Apr 06, 2023
Contact name Juanjo Lozano
E-mail(s) juanjo.lozano@ciberehd.org
Organization name CIBEREHD
Department Plataforma de Bioinformatica
Street address C/ Rosselló 153
City Barcelona
ZIP/Postal code 08036
Country Spain
 
Platform ID GPL17303
Series (1)
GSE199168 CXCR4 DRIVES HEPATOCYTE REPROGRAMMING IN ALCOHOL-RELATED LIVER DISEASE
Relations
BioSample SAMN26871140
SRA SRX14566330

Supplementary file Size Download File type/resource
GSM5965591_TXs_129RD_2_A_IE02.IonXpress_002.count.txt.gz 231.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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