|
| Status |
Public on Nov 05, 2023 |
| Title |
P42_IBCs_IPhs_10x |
| Sample type |
SRA |
| |
|
| Source name |
Mixture of many wild type cochlear cell types
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Cochlea
age: postnatal day 42
genotype: Plp1-CreER+; Ai9/+
|
| Treatment protocol |
WT-Cochlear IHCs-P30 (#1-#26) were obtained from vGlut3-P2A-iCreER/+; Ai9/+ mice that were administered tamoxifen at P10 and P11, and sacrificed at P30. P42_IBCs/IPhs_10x cells were obtained from Plp1-CreER+; Ai9/+ mice that were administered tamoxifen at P0 and P1, and sacrificed at P42. P42_new IHCs_10x cells were obtained from Plp1-TAT-DTR mice that were adminstered tamoxifen at P0 and P1, DT at P2, TMP at P3 and P4, and were finally sacrificed at P42.
|
| Growth protocol |
N/A
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cell dissociation protocal was described in our previous studies (PMID: 29706463, and PMID: 26472907)
Smart-Seq HT kit (Cat# 634437, Takara) was used to generate full-length cDNA. The cDNAs (1 ng each) were tagmented using a TruePrep DNA Library Prep Kit V2 for Illumina (Cat# TD503-02, Vazyme) and a TruePrep Index Kit V2 for Illumina (Cat# TD202, Vazyme).
Single cell full length cDNA RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FastQC (v0.11.9) and Trimmomatic (v0.39) were used for quality control. Reads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.1.0) with default parameters.
Transcript Per Million (TPM) were calculated by StringTie (v1.3.5) with default parameters.
Raw counts were calculated by HTSeq (v0.10.0) software.
Cell Ranger (v3.0.2) was used for analysis of 10x libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for smartseq. Feature-barcode-matrix output from Cell Ranger for 10x data.
|
| |
|
| Submission date |
Nov 05, 2021 |
| Last update date |
Nov 05, 2023 |
| Contact name |
Minhui Ren |
| E-mail(s) |
mhren@ion.ac.cn
|
| Phone |
0086-21-54921793
|
| Organization name |
Institution of Neuroscience, CAS
|
| Street address |
320 Yueyang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE188259 |
In situ regeneration of inner hair cells in the damaged cochlea by temporally regulated coexpression of Atoh1 and Tbx2 |
|
| Relations |
| BioSample |
SAMN22929165 |
| SRA |
SRX12997056 |
