|
| Status |
Public on Aug 13, 2018 |
| Title |
PP1_3 |
| Sample type |
SRA |
| |
|
| Source name |
Progenitot population type 1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse femur
cell type: Periosteal progenitor cells
strain: C57/B6
age: Day 6
genotype: CTSK-cre+ mTMG
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Skeletal tissue from postnatal day 6, mice was subjected to both mechanical and enzymatic digestion. Single cells were obtained, stained for Flow cytometry antibodies and FACS was conducted to sort the desired cell types. RNA samples were prepared using the RNeasy Plus Micro kit Cat no 74034.
cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit and sequenced on HiSeq4000 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC mm10 mouse reference genome using tophat v2.0.11.
Raw reads counts were extracted using htseq-count v0.6.1.
Differential expression analysis was performed by using DESeq2 package v1.6.3.
Genome_build: mm10
Supplementary_files_format_and_content: excel file including gene name, Ensembl gene id, normalized read counts for each gene in each sample
|
| |
|
| Submission date |
Oct 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew Greenblatt |
| E-mail(s) |
matt.greenblatt@gmail.com
|
| Organization name |
WEILL CORNELL MEDICAL COLLEGE
|
| Department |
Pathology and Laboratory Medicine
|
| Street address |
1161 York Ave APT 1a
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE106235 |
Discovery of a periosteal stem cell mediating intramembranous bone formation and fracture healing (batch RNA-Seq) |
| GSE106237 |
Discovery of a periosteal stem cell mediating intramembranous bone formation and fracture healing |
|
| Relations |
| BioSample |
SAMN07839218 |
| SRA |
SRX3333143 |
