 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 27, 2024 |
| Title |
20220307_M41_WT_13Gy_FLASH_5M_2626 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
treatment: FLASH IR
|
| Treatment protocol |
Mice were irradiated after 2 consecutive days of AsiDNA injections (100mg/kg), followed by a third day with AsiDNA injection (200mg/kg) and FLASH/CONV irradiation.
|
| Growth protocol |
Lungs were collected 5 months following radiotherapy and drug treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The trachea of the mouse was perfused with 1.5 ml of 50 U/ml dispase using, followed by 0.5 ml of 1% agarose. Lungs were minced using a scalpel to create small pieces and added into 3 ml of 1× DPBS MgCl2+and CaCl2+. Then 320 µl of 25 U/ml elastase were added and the suspension was homogenized at 37 °C using orbital shaking. The suspension was treated with 1× DPBS containing 10% fetal bovine serum (FBS) and 20 µl of 0,5 M EDTA pH 8 and filtered through 100 µm nylon cell strainer. The cells were treated with 37.5 µl of 10 mg/ml DNase I on ice, filtered through a 40 μm nylon cell strainer, centrifuged, resuspended in red blood cell (RBC) lysis buffer and incubated at RT before inhibition of the lysis using PF10 supplementation. After centrifugation, the pellet was resuspended in 1 ml of 1× DPBS containing 0.02% bovine serum albumin (BSA). Concentration of the samples was adjusted to 1 million cells/ml in 1× DPBS containing 0,02% BSA.
Library was performed according to the manufacter's instructions (single cell 3' v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beats into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values and matrix files
|
| |
|
| Submission date |
Aug 09, 2023 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Anouk Sesink |
| E-mail(s) |
anouk.sesink@curie.fr
|
| Organization name |
Institut Curie
|
| Street address |
Rue Henri Becquerel
|
| City |
Orsay |
| ZIP/Postal code |
91401 |
| Country |
France |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE240510 |
The AsiDNA™ decoy mimicking DSBs protects the normal tissue from radiation toxicity through a DNA-PK/p53/p21-dependent G1/S arrest. |
|
| Relations |
| BioSample |
SAMN36918821 |
| SRA |
SRX21320057 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7699258_20220307_M41_WT_13Gy_FLASH_5M_2626.csv.gz |
13.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
