|
| Status |
Public on Dec 27, 2018 |
| Title |
Bulk_pre-DC_rep2 [307_AAGAGG] |
| Sample type |
SRA |
| |
|
| Source name |
Bulk_pre-DC [Bulk RNA-seq]
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
developemental stage: E15.0
tissue: backskin
cell type: pre-DC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA obtained from FACS-sorted cells was purified with the Absolutely RNA Nanoprep kit (Agilent), quantified with the NanoDrop spectrophotometer (Thermo Scientific) and measured for quality control by the Agilent Bioanalyzer. Samples with RIN (RNA integrity number) scores 8.8 and higher were further processed. 6ng starting material was reverse transcribed and amplified to 5-7µg cDNA with the RNA Ovation RNA-seq System V2 (NuGEN).
From 100ng amplified cDNA sequencing libraries were generated with 16 unique barcoded adapters (8 samples x 2 replicates) using the Ovation Ultralow DR Library System (NuGEN).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file : E15.0_bulkRNAseq_Final.xlsx
307_AAGAGG
|
| 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 |
GPL13112 |
| Series (1) |
| GSE122026 |
Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent |
|
| Relations |
| BioSample |
SAMN10354860 |
| SRA |
SRX4961699 |
