|
| Status |
Public on Jul 20, 2021 |
| Title |
E12.5 inv2 posterior proximal forelimb, replicate 2 scRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
posterior proximal forelimb
|
| Organism |
Mus musculus |
| Characteristics |
age: E12.5
strain: B6CBAF1
genotype: inv2
tissue: posterior proximal forelimb
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Crosses were made between heterozygous adults. Animals were checked for vaginal plugs on the next morning, establishing the timepoint 0.5 embryonic days. Embryos were collected 12 days later.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Embryos were collected and stored in 1X PBS treated with DEPC and held on ice while genotyping was performed. Embryos with the desired genotype were selected and the posterior portion of each of the forelimbs was isolated for each replicate (1 replicate is the pool of left and right forearm cells). The cells were digested in collagenase and stored in 1X PBS containing 10% FCS and 0.2mM EDTA to prevent cellular aggregation. The cells samples were transferred to the EPFL Gene Expression Core Facility for preparation into 10X GEMs and reverse transcription according to the 10X Chromium 3.1 protocol.
Libraries were constructed with the 10X Chromium 3.1 protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
10x 3.1 scRNA-seq
|
| Data processing |
Sequencing reads were processed with Cell Ranger 3.1.0 for demultiplexing, barcode processing, and 3' gene counting using a modified gene annotation file (10.5281/zenodo.4456702).
Genome_build: mm10
Supplementary_files_format_and_content: archive containing the output of Cell Ranger (features.tsv.gz, barcodes.tsv.gz, matrix.mtx.gz)
|
| |
|
| Submission date |
Jan 25, 2021 |
| Last update date |
Jul 20, 2021 |
| Contact name |
Lucille Lopez-Delisle |
| E-mail(s) |
lucille.delisle@epfl.ch
|
| Organization name |
EPFL
|
| Street address |
Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE165494 |
Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations [scRNA-seq] |
| GSE165495 |
Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations |
|
| Relations |
| BioSample |
SAMN17551429 |
| SRA |
SRX9934287 |
