|
Status |
Public on Oct 07, 2017 |
Title |
infected_T2_71 |
Sample type |
SRA |
|
|
Source name |
BMDM
|
Organism |
Mus musculus |
Characteristics |
cell culture: primary cell culture agent: Salmonella typhimurium SL1344 time point: 2.5h strain: C57BL/6
|
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
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
T2_TC_sample_0167
|
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 a combined transcriptome of mouse downaloaded from UCSC genome browser (GRCM38/mm10) and salmonella from NCBI NC_017718.1 (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) |
GSE102160 |
Single cell RNA Seq data of BMDM from mouse infected with Salmonella [full time course] |
GSE102163 |
Single cell RNA Seq data of BMDM from mouse infected with Salmonella |
|
Relations |
BioSample |
SAMN07440952 |
SRA |
SRX3055704 |