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| Status |
Public on Apr 28, 2021 |
| Title |
NeuroD_rep2_lacz |
| Sample type |
SRA |
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| Source name |
NeuroD_lacz
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| Organism |
Ciona intestinalis |
| Characteristics |
developmental stage: late tailbud II
treatment: electroporated with Dmrt1>H2B:GFP and Dmrt1>Lacz
tissue/cell type: whole embryos
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| Treatment protocol |
After fertilization using gametes from the same individual, one-cell stage embryos were electroporated with Dmrt1>H2B:GFP and Dmrt1>LacZ (control condition) or Dmrt1>H2B:GFP and Dmrt1>NeuroD (NeuroD overexpression condition).
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| Growth protocol |
Adult Ciona intestinalis (Pacific species also named Ciona robusta) collected in the Pacific Ocean were purchased from M-Rep San Diego, CA and MarinUS, Long Beach, CA. The gametes were collected as previously described in Christiaen et al, 2009.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
At the late tailbud stage I, morphologically normal embryos were selected, and at late tailbud II, GFP+ embryos were dissociated as previously described in Cao et al, 2019. The dissociation was performed in duplicate. The cell concentration of each sample was checked by TC20 Automated Cell Counter to ensure it was within 1,000–2,000 cells per microlitre. Single-cell suspensions were loaded onto The Chromium Controller (10x Genomics). For all of the samples, cells were lysed, cDNAs were barcoded and amplified with Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10x Genomics) following the instructions of the manufacturer.
Illumina sequencing libraries were prepared from the cDNA samples using the Nextera DNA library prep kit (Illumina). All of the libraries were sequenced on Illumina NovaSeq 6000 with S1 reagent kit (300 cycles, paired-end) following standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing reads were filtered by Illumina NovaSeq Control Software and only pass-filtered reads were used for further analysis.
Reads that aligned to phix (using Bowtie version 1.1.1) were removed, as were reads that failed Illumina’s default chastity filter.
We then combined the FASTQ files from each lane and separated the samples using the barcode sequences allowing one mismatch (using barcode_splitter version 0.18.2).
In the read 2 of each sample, the rightmost bases after to position 100 were trimmed to keep only high-quality reads.
Using 10x CellRanger version 3.0.2, the count pipeline was run with default settings on the trimmed FASTQ files to generate gene–barcode matrices for each sample. The integration of scRNA-Seq data of NeuroD overexpressed embryos and the control embryos were performed with Seurat v3.0
Genome_build: KH gene models (ver.2013, http://ghost.zool.kyoto-u.ac.jp/download_kh.html)
Supplementary_files_format_and_content: gene–barcode matrices; Hierarchical Data Format
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| Submission date |
Feb 04, 2021 |
| Last update date |
May 01, 2021 |
| Contact name |
Chen Cao |
| E-mail(s) |
chencao@princeton.edu
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| Organization name |
Princeton University
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| Department |
Lewis-Sigler Institute for Integrative Genomics
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| Lab |
Levine Lab
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| Street address |
Icahn lab
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| City |
Princeton |
| State/province |
New Jersey |
| ZIP/Postal code |
08550 |
| Country |
USA |
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| Platform ID |
GPL29701 |
| Series (1) |
| GSE166235 |
The hypothalamus predates the origin of vertebrates |
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| Relations |
| BioSample |
SAMN17804601 |
| SRA |
SRX10035216 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5066622_Lacz_rep2_filtered_feature_bc_matrix.h5 |
22.8 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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