|
| Status |
Public on May 05, 2021 |
| Title |
LN_MS-1 |
| Sample type |
SRA |
| |
|
| Source name |
LN_MS-1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
organ: lymph node
cell type: mixed -whole tissue
selection marker: none
age: 6 weeks
Sex: female
treatment: MS
|
| Treatment protocol |
mice were injected with either PBS or Mycobacterium smegmatis (Ms) for 48 hr
|
| Growth protocol |
n/a
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Auricular LNs were digested in IMDM containing 100 µg/mL Liberase TL and 100 µg/mL DNase I (both from Roche, Germany) for 20 minutes at 37°C. Last 5 minutes of incubation, EDTA was added at a final concentration of 10 mM. Cells were collected, filtered through a 70mm cell strainer, washed with PBS + 0.04% BSA for a final concentration of 1000 cells/µL.
10x genomics v3.1 dual index
10x genomics single cell 3' RNA-seq 3’ : 28bp R1 and 90 bp R2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
injection of MS 48 hr prior to experiment
|
| Data processing |
10x genomics pipeline
mm10
Genome_build: refdata-cellranger-mm10-1.2.0.tar.gz
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
|
| |
|
| Submission date |
May 03, 2021 |
| Last update date |
May 06, 2021 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
|
| Phone |
972-8-9343338
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Immunology
|
| Street address |
234 Herzl st.
|
| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE173774 |
Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation (scRNA-Seq) |
| GSE173778 |
Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation |
|
| Relations |
| BioSample |
SAMN18988648 |
| SRA |
SRX10760614 |
