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Sample GSM5240033 Query DataSets for GSM5240033
Status Public on Oct 02, 2023
Title HEL control 1
Sample type SRA
 
Source name HEL
Organism Homo sapiens
Characteristics cell line: HEL
treatment: none
replicate: replicate 1
group: control
Treatment protocol Cells in treatment group were either treatded with 4-hydroxytamoxifen or vehicle control for 4 hours
Growth protocol HEL cells were cultured in phenol red-free RPMI-1640 medium supplemented with 10% Charcoal Stripped fetal bovine serum and antibiotics. UKE-1 cells were cultured in phenol red-free IMDM medium supplemented with 10% Charcoal Stripped fetal bovine serum , antibiotics (penicillin, 100 I.U./ml; streptomycin, 100 µg/ml), 10% heat-inactivated horse serum (HS) and 1 μM hydrocortisone
Extracted molecule polyA RNA
Extraction protocol RNA was isolated by Trizol Reagent, then clean-up by RNeasy Mini Column.
The libraries were prepared from 500ng total RNA with the NEB Ultra II directional RNA seq kit, with a PolyA selection, and ERCC spike ins.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description In vitro cell culture
Data processing The quality control checks of raw sequencing data was performed using fastqc.
The alignment of processed reads against the GRCm38, Mus musculus, reference genome were performed using HISAT2.
The aligned sam files were sorted and converted to bam format using SAMtools, the transcript-based expression was quantified using featurecounts.
the normalisation and diffeerntial expression analysis was performed using DESeq2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: normalized expression level matrix (CPM)
 
Submission date Apr 13, 2021
Last update date Oct 02, 2023
Contact name Irina Mohorianu
E-mail(s) data-submissions@stemcells.cam.ac.uk
Organization name University of Cambridge
Department Wellcome-MRC Cambridge Stem Cell Institute
Street address Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
 
Platform ID GPL20301
Series (2)
GSE172023 RNAseq of JAK2V617F-positive MPN cell lines after 4-Hydroxytamoxifen treatment
GSE172025 RNA-seq of Myeloproliferative neoplasms primary CD34+ HSPCs and cell lines after tamoxifen treatment
Relations
BioSample SAMN18736921
SRA SRX10596412

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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