|
| Status |
Public on Mar 30, 2022 |
| Title |
LN6-987AL scRNA LN |
| Sample type |
SRA |
| |
|
| Source name |
lymph node
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
|
| Growth protocol |
All cell lines are grown in DMEM supplemented with 10% FBS, glutamine, and penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell lines were trypsinized, washed with complete serum, centrifuged, and washed with PBS. Following washing cell pellets were frozen at -80C. After thawing, cells were resuspended in buffer RLT and lysed using QiaShredders. Extraction was performed using the Qiagen RNEasy Plus mini kit according to the manufacturer's protocol.
Library construction (RNA-seq) was performed by MedGenome using the Illumina TruSeq stranded mRNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
LNs were harvested in HBSS supplemented with 2% FBS (HBSSF) on ice. LNs were subjected to mincing and digestion with Collagenase 4 (Worthington) in RPMI-1640 for 10 minutes at 37°C prior to dissociation on 70μm strainers. Suspensions were washed twice with HBSSF, counted, and resuspended in PBS + 0.04% bovine serum albumin (Sigma). 10X Genomics library preparation was performed according to the manufacturer’s protocol by the Stanford Genome Sequencing Service Center.
|
| Data processing |
Raw sequencing reads were filtered and adapters trimmed using Trimmomatic v0.36. Quality was assessed using FastQC v0.11.3.
Transcript abundance was quantified using Salmon v0.7.2 in quasi-mapping mode and using the sequence, GC, and position bias correction parameters.
Differential expression analysis was performed using DESeq2.
Assembly: GRCm38 GENCODE release M11
Supplementary files format and content: tab-delimeted files contain TPM values for each sample generated by Salmon
|
| |
|
| Submission date |
Mar 29, 2022 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Nathan Edward Reticker-Flynn |
| E-mail(s) |
naterf@stanford.edu, retickerflynn@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Pathology
|
| Lab |
Engleman Lab
|
| Street address |
3373 Hillview Ave
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE117529 |
RNA/WES/ATAC/scRNA sequencing of murine melanoma primary and LN metastases |
|
| Relations |
| BioSample |
SAMN27064474 |
| SRA |
SRX14660743 |
