|
| Status |
Public on Oct 15, 2015 |
| Title |
Co_PCP_100_Epit |
| Sample type |
SRA |
| |
|
| Source name |
Cochlear epithelium
|
| Organism |
Mus musculus |
| Characteristics |
purification: Enzymatic/mechanical
c1 ifc #: IFC 5
gfp (i): N/A
tdtomato (i): N/A
classifications: Cochlear epithelium bulk population
|
| Treatment protocol |
All cells are untreated.
|
| Growth protocol |
All cells used were from acute isolations from postnatal day 1 mice that carry transgenic alleles to fluorescently mark the supporting cells and hair cells of the inner ear.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Following dissociation of tissue into a single-cell suspension, target cells were enriched by purification as described, cells were lysed, polyA RNA reverse-transcribed, and cDNA amplified using SMARTer ultra-low input cDNA synthesis (Clontech) on the C1 microfluidics platform (Fluidigm).
cDNA libraries were prepared for sequencing using Nextera XT tagmentation and 96-barcode indexing (Illumina). Barcoded samples were pooled, cleaned with Agencourt AMPure XP magnetic bead isolation (Beckman Coulter).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
100-200 cell bulk population
|
| Data processing |
Basecalling and sample demultiplexing by Illumina HAS 0.9
We prepared a Bowtie2_2.2.3 index from the NCBI whole genome mm10 reference transcriptome using default rsem1.2.19 parameters
Paired-end reads were aligned to transcriptome using rsem1.2.19 command rsem-calculate-expression -p 16 --calc-pme --calc-ci --ci-memory 20000 --bowtie2 --bowtie-chunkmbs 512 --no-bam-output --time --paired-end --forward-prob 0.5 --estimate-rspd *R1_001.fastq *R2_001.fastq /ReferenceLocation ./OutputLocation 2>./*.Log.txt 1>./*.Console.txt
Genome_build: NCBI GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file with the estimated expression (TPM) for each gene for each Sample as calculated by RSEM1.2.19. Tab-delmited text file with the estimated count for each gene for each Sample as calculated by RSEM1.2.19.
|
| |
|
| Submission date |
Aug 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael C Kelly |
| E-mail(s) |
michael.kelly3@nih.gov
|
| Organization name |
NCI
|
| Department |
Center for Cancer Research
|
| Lab |
Single Cell Analysis Facility
|
| Street address |
41 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20894 |
| Country |
USA |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE71982 |
Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear |
|
| Relations |
| BioSample |
SAMN03983065 |
| SRA |
SRX1142777 |
