|
| Status |
Public on Dec 27, 2018 |
| Title |
SC_KM05 [Single Cell RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Single Cell RNA-seq
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
developemental stage: E15.0
tissue: backskin
cell type: single cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted into 5µl Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius for 5 minutes. mRNA was then reverse transcribed by adding RT mix.
RNA was processed by SORT-Seq, an automated version of the previously described Cel-Seq2 technique. Libraries were sequenced on a Illumina NextSeq500 using 75bp paired end sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file : E15.0_Mesenchymal cells_scRNAseq_Final.csv
KM05_AHN5JMBGX3_S2
|
| Data processing |
(Bulk RNA-seq) All raw RNA sequencing reads were mapped to the mouse genome (mm10) with TopHat v2.0.3 coupled with the Bowtie2 aligner with default parameters. Transcriptomes were assembled and fragments per kilo-base per million reads (FPKM) for each gene were computed with Cufflinks v2.1.1 with default parameters.
(Single Cell RNA-seq) Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mm10 mouse genome release downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Genome_build: mm10
Supplementary_files_format_and_content:
(Bulk RNA-seq) E15.0_bulkRNAseq.xlsx: Tab separated file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples. Column name indicates the sorted cell type (each sorted cell type has two biological replicates). The first column lists the official gene symbol.
(Single Cell RNA-seq) E15.0_Mesenchymal cells_scRNAseq.csv: Tab separated data file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples (including 16 blank wells/plate, called ERCC). Column name indicates the cell type determined from index sorting, sample number,followed by the cell number of the library, all separated by underscores (i.e. Cell Type_Sample_Cell Number). The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
|
| |
|
| Submission date |
Oct 31, 2018 |
| Last update date |
Dec 27, 2018 |
| Contact name |
Michael Rendl |
| E-mail(s) |
michaelrendl@gmail.com
|
| Organization name |
Mount Sinai School of Medicine
|
| Street address |
1428 Madison Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE122026 |
Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent |
|
| Relations |
| BioSample |
SAMN10354847 |
| SRA |
SRX4961714 |
