|
| Status |
Public on Apr 30, 2023 |
| Title |
verteral Emb+GFP+ biol rep 2 [s166] |
| Sample type |
SRA |
| |
|
| Source name |
spine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spine
cell line: primary vertebral cells
cell type: GFP+CD31-TER119-CD45-Thy-6C3-CD200+CD105-EMB+
genotype: WT
Sex: male
developmental stage: postnatal day 10
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). RNA quality and quantity were verified by using an Agilent 2100 Bioanalyzer system.
cDNA libraries were generated using the Illumina SMART-Seq v4 plus Nextera XT DNA Library Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
fpkm.genes.ensembl_id.protein_coding.txt
|
| Data processing |
The samples were sequenced using Illumina NovaSeq6000 sequencer with paired-end 100 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples
|
| |
|
| Submission date |
Apr 27, 2023 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Genomics-core-facility WCM |
| E-mail(s) |
[email protected]
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
1300 York Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE230724 |
Transcriptional profiling of EMB+ cells and EMB- cells across long bone and vertebrae |
|
| Relations |
| BioSample |
SAMN34395678 |
| SRA |
SRX20116990 |
