|
| Status |
Public on Jul 24, 2017 |
| Title |
MR-scRNAseq-40080044-cell-30 |
| Sample type |
SRA |
| |
|
| Source name |
single MEF cell, 1 Gy irradiation, no micronuclei
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
cell type: MEF
treatment: 1 Gy irradiation, no micronuclei
passed qc and used in paper: TRUE
|
| Treatment protocol |
Cells were irradiated (1 Gy) and re-seeded onto 50 mm PEN membrane dishes (Zeiss) 32 h later. Picogreen-containing medium (Quant-iT PicoGreen dsDNA reagent, 4 μl per ml) was added to the cells 48 h post-IR to stain DNA, and laser capture microdissection (LCM) performed
|
| Growth protocol |
MEFs were grown in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 μg/ml streptomycin and 0.1 mM β-mercaptoethanol at 37°C in 5% CO2 and 3% O2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Individual cells were captured in 5 μl 0.2% (v/v) Triton-X100, 2 U/μl RNasin Ribonuclease Inhibitor (Promega) and cDNA obtained using the Smart-seq2 protocol
NextSeq550 with Nextera dual indexing
Single Cell RNA-Seq (NextSeq550)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
MR32
|
| Data processing |
Fastq files were aligned against GRCm38.p5 reference mouse genome obtained from the Ensembl database using STAR RNA-seq aligner
Quantification of mapped reads for genomic features was calculated using Rsubread
Gene zero counts were excluded and QC matricies (paramaters set to exclude cells with ERCC >10%, gene features < 2000 and total counts <40,000) were calculated using the R package scater to create final feature counts file: MR-scRNAseq-40080044_35-cells_Feature_counts.csv
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: feature counts
|
| |
|
| Submission date |
Jul 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Vittorio Sebastiano |
| E-mail(s) |
vsebast@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
OB-GYN/Reproductive, Perinatal and Stem Cell Biology Research
|
| Lab |
Sebastiano Lab
|
| Street address |
265 Campus Drive
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5454 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE100771 |
cGAS surveillance of micronuclei links genome instability to innate immunity |
|
| Relations |
| BioSample |
SAMN07312806 |
| SRA |
SRX2980446 |
