|
Status |
Public on Jun 13, 2024 |
Title |
MDMs, Normoxia_day2_rep3 |
Sample type |
SRA |
|
|
Source name |
Monocyto-derived macrophages
|
Organism |
Homo sapiens |
Characteristics |
tissue: Monocyto-derived macrophages individual: Healthy donor 3 treatment: Normoxia
|
Treatment protocol |
Hypoxic cell culture was performed in a Whitley H35 Hypoxystation at 37 °C, 5% CO2, 1 % O2and 94% N2.
|
Growth protocol |
Monocyte derived macrophages were maintained in RPMI supplemented with 10% Human AB serum.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from MDM using the RNeasy Plus minikit. RNASequencing libraries were generated using the SMARTer Stranded Total RNA-Seq v2 - Pico Input Mammalian kit (Takara).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Quality trimming, to remove adapter sequences and check for low quality base calling, was performed with TrimGalore Transcript quantification was performed using Salmon Differential transcript analysis was performed with DESeq2 Assembly: Gencode Human Release 35 (GRCh38.p13) Supplementary files format and content: Salmon quant files that contain TPM values for each transcript
|
|
|
Submission date |
Jun 12, 2024 |
Last update date |
Jun 13, 2024 |
Contact name |
Niek Wit |
E-mail(s) |
nw416@cam.ac.uk
|
Organization name |
University of Cambridge
|
Department |
Department of Medicine
|
Lab |
Professor James Nathan
|
Street address |
Puddicombe Way
|
City |
Cambridge |
State/province |
Not US or Canada |
ZIP/Postal code |
CB2 0AW |
Country |
United Kingdom |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE269699 |
Hypoxia drives HIF2-dependent reversible macrophagecellcycle entry |
|
Relations |
BioSample |
SAMN41807509 |
SRA |
SRX24895351 |