|
| Status |
Public on Mar 21, 2024 |
| Title |
LepR+ Pressfit Bone [Sample_LepR.plus.4_L002] |
| Sample type |
SRA |
| |
|
| Source name |
Pressfit
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Pressfit
cell type: Bone
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
LEPR+ cells obtained from peri-implant bone or fibrous tissue from mouse undergoing tibia implantation. Single cells were obtained, stained for Flow cytometry antibodies and FACS was conducted to sort the desired cell types. RNA sample were prepared using the RNAeasy Plust Micro Kit Cat no 74034. cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit and sequenced on NovaSeq 6000 sequencer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample_LepR.plus.4_L002
|
| Data processing |
Detailed pipeline description and parametrization is available at https://gitlab.com/hssgenomics/pipelines/-/tree/master/RNAseq . Briefly, Read quality was assessed and adaptors trimmed using FASTP. Reads were then mapped to thehuman genome (hg38) and reads in exons were counted against Gencode with STAR2.6 Aligner. Differential gene expression analysis was performed in R using edgeR. Genes with low expression levels (<3 counts per million in at least one group) were filtered from all downstream analyses. Differential expression was estimated using quasi-likelihood framework. Benhamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with an FDR-corrected pvalue less than 0.05 were considered differentially expressed. Downstream analyses were performed in R using a visualization platform built with Shiny developed by bioinformaticians at the David Z. Rosensweig Genomics Research Center at HSS
Assembly: mm10
Supplementary files format and content: comma separated text files of counts for each sample
|
| |
|
| Submission date |
Mar 21, 2023 |
| Last update date |
Mar 21, 2024 |
| Contact name |
HSS Genomics Research Center |
| Organization name |
Hospital for Special Surgery
|
| Department |
Research
|
| Street address |
535 E 70th St
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE227869 |
Transcriptomic profile of Lin negative, LEPR positive cells of murine peri-implant fibrous tissue and peri-implant bone |
|
| Relations |
| BioSample |
SAMN33845650 |
| SRA |
SRX19742237 |
