|
| Status |
Public on Oct 07, 2017 |
| Title |
singles_unexposed_30 |
| Sample type |
SRA |
| |
|
| Source name |
BMDM
|
| Organism |
Mus musculus |
| Characteristics |
cell culture: primary cell culture
strain: C57BL/6
time point: 0
agent: unexposed
|
| Treatment protocol |
BMDMs were infected at an MOI of 50:1. After 30 minutes, cells were washed with media containing 15 μg/ml gentamicin.
|
| Growth protocol |
C57BL/6 WT mice were obtained from Jackson Laboratory. Cultures of Salmonella typhimurium labeled with GFP (pFPV25.1; Addgene) were grown in Luria-Bertani (LB) medium at 37°C, washed in PBS and incubated for 1 hr with pHrodo dye (Life Technologies)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
From each time-point cells were lifted from plates and sorted using fluorescence activated cell sorting (FACS) into 96-well plates containing 4.5 μl lysis buffer (TE containg 5%NP-40 and RNAse inhibitor) (Avraham et al., 2015).
scDual-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
cells_singles_cells_unexposed_sample_0030
|
| Data processing |
Libraries were sequenced on the Illumina HiSeq2500, paired-end sequencing R1- 15bp, R2- 35bp, Index- 6bp
Conversion from BCL to FASTQ and deumltiplexing using CASAVA
Filter barcode minimum quality of 10.
Demultiplexing using the CEL-Seq2 pipeline (Hashimshony, et a. 2016) of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against mouse and salmonella transcriptome from refseq (Avraham et al., 2015)
Genome_build: Read counting with htseq-count
Supplementary_files_format_and_content: expression matrix
|
| |
|
| Submission date |
Aug 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Itai Yanai |
| E-mail(s) |
Itai.Yanai@nyumc.org
|
| Organization name |
New York University, School of Medicine
|
| Department |
Biochemistry and Molecular Pharmacology
|
| Lab |
Itai Yanai
|
| Street address |
430 East 29th St., Office 510
|
| City |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE102161 |
Single cell RNA Seq data of BMDM from mouse infected with Salmonella [hundred_ten_singles] |
| GSE102163 |
Single cell RNA Seq data of BMDM from mouse infected with Salmonella |
|
| Relations |
| BioSample |
SAMN07440712 |
| SRA |
SRX3055515 |
