|
| Status |
Public on Oct 02, 2023 |
| Title |
UKE1 cell control 1 |
| Sample type |
SRA |
| |
|
| Source name |
UKE1 cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: UKE1
treatment: with HS
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 |
SAMN18736915 |
| SRA |
SRX10596400 |
