|
| Status |
Public on Oct 16, 2023 |
| Title |
Cereblon_Overexpression, scRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Ciona intestinalis type A
|
| Organism |
Ciona intestinalis |
| Characteristics |
tissue: Mid tailbud embryo
genotype: Tbx6b>Crbn-T2A-GFPCAAX
|
| Treatment protocol |
Fertilized eggs were electroporated with either plasmids coding for a membrane GFP expressed in the tail muscle (Tbx6b>T2A-GFPCAAX, control condition) or plasmids coding for Cereblon and a membrane GFP expressed in the same tissue (Tbx6b>Crbn-T2AGFPCAAX, Crbn overexpression condition). Once the fluorescence could be detected, morphologically heathly GFP+ embryos were selected.
|
| Growth protocol |
Gametes from Ciona intestinalis type A were collected as described by Christians and Collegeagues in 2009. Fertilized eggs were electroporated (see treatment protocol) and grow until the mid tailbud stage.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mid tailbud embryos were dissociated into single cells using trypsin in sea water following the protocol published by Cao and colleagues in 2019.
Between 1000 and 2000 cells per condition were loaded onto the Chromium Controller (10x Genomics). The cells were lysed, the polyA RNA was retro-transcribed, barcoded with the Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10x Genomics) using the protocols provided by the manufacturer. Nextera DNA library prep kit (Illumina) was used to construct Illumina sequencing libraries from amplified cDNA. The libraries were then sequenced on a Illumina NovaSeq 6000 instruments with the SP reagent kit (100 cycles, paired-end).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Single cell RNA sequencing from Ciona mid tailbud embryos expressing in the tail muscle GFP targeted to the membrane and Cereblon (Crbn)
|
| Data processing |
Filtering, quality control of the raw sequencing and generation of the FASTQ files were performed as described by Cao and colleagues in 2019. Briefly, the raw sequencing reads were filtered by Illumina NovaSeq Control Software. Reads aligning to phix using Bowtie version 1.1.1 and those falling the default chastity filter of Illumina were removed. To separate control and Crbn overexpression conditions, the reads were demultiplexed using barcode_splitter version 0.18.2, allowing one mismatch in the barcode.
To generate the gene barcode matrices, the FASTQ files were processed with 10x Cell Ranger version 3.0.0.
Assembly: Ciona intestinalis type A KH gene models (ver.2013, http://ghost.zool.kyoto-u.ac.jp/download_kh.html)
Supplementary files format and content: gene barcode matrices
|
| |
|
| Submission date |
Aug 29, 2023 |
| Last update date |
Oct 16, 2023 |
| Contact name |
Laurence A. Lemaire |
| E-mail(s) |
laurence.lemaire@slu.edu
|
| Organization name |
Saint Louis University
|
| Department |
Biology
|
| Lab |
Lemaire
|
| Street address |
3507 Laclede Ave
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63103 |
| Country |
USA |
| |
|
| Platform ID |
GPL29701 |
| Series (1) |
| GSE241857 |
Cereblon influences the timing of muscle differentiation in Ciona tadpoles |
|
| Relations |
| BioSample |
SAMN37185958 |
| SRA |
SRX21503234 |
