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Sample GSM7507976 Query DataSets for GSM7507976
Status Public on Jan 24, 2024
Title LSECs; citrate buffer-injected mouse, rep. 1
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics tissue: Liver
cell line: LSECs
cell type: FAC-sorted LSECs (CD45-dim, STAB2-high, CD146-high)
genotype: wild type
treatment: intravenous injection with citrate buffer (0,05M) for 5 hours
Treatment protocol n/a
Growth protocol n/a
Extracted molecule total RNA
Extraction protocol RNA from sorted LSECs was extracted using TRIzol™ LS Reagent (ThermoScientific, #10296028) according to the manufacturer’s instructions with an additional step of RNA precipitation with glycogen (ThermoScientific, #R0551).
Library was prepared using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit according to the manufacturer’s protocol (Thermo Fisher Scientific)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description female Balb/c mouse
Data processing The raw reads were processed with Ion Torrent RNASEQAnalysis pipeline (Torrent Suite version 5.0.4)
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
Assembly: AmpliSeq Mouse Transcriptome v1
Supplementary files format and content: htseq normalized count
 
Submission date Jun 23, 2023
Last update date Jan 24, 2024
Contact name Michał Mikula
E-mail(s) mikula.michal@gmail.com
Phone +48225462655
Organization name Maria Skłodowska-Curie National Research Institute of Oncology
Department Genetics
Street address Roentgena 5
City Warsaw
ZIP/Postal code 02781
Country Poland
 
Platform ID GPL18635
Series (2)
GSE235692 NRF2-independent iron-triggered signaling via MAPK p38-ETS1 regulates LSEC Bmp6 mRNA expression [I]
GSE235976 NRF2-independent iron-triggered signaling via MAPK p38-ETS1 regulates LSEC Bmp6 mRNA expression
Relations
BioSample SAMN35881687
SRA SRX20765461

Supplementary file Size Download File type/resource
GSM7507976_2L_Bufor2.counts.txt.gz 101.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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