|
| Status |
Public on Feb 08, 2023 |
| Title |
1B neuron, seqment A7, animal 7, cell d225051 |
| Sample type |
SRA |
| |
|
| Source name |
neuron
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: neuron
segment: A7
cell type: 1B
animal: 7
gender: M
strain: w[1118]
genotype: GMR94G06-GAL4>10XUAS-IVS-mCD8::GFP
|
| Growth protocol |
Fly stocks were raised at 25°C on standard molasses food in an incubator with 12 hrs day/night cycle. Actively crawling 3rd instar larvae that are size and age matched were used for all experiments.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cellular material was aspirated in whole-cell patch electrodes and transferred to 384 well plates followed by extraction with XXX
RNAseq libraries from single cells were prepared using a modified version of the SMART-seq2 single-cell protocol (Picelli et al., 2013, Trombetta et al., 2014). RNA from single cells was placed in Hard-Shell 384-well plates (Catalog #HSP3801) in minimal volume (<2uL). cDNA was prepared following the standard protocol using 1/3 of the recommended volumes for all reagents utilizing a Mosquito HV automated liquid handler (SPT Labtech). Amplified cDNA was purified using 0.75X SPRI beads, quantified using picogreen and spot-checked on the Fragment Analyzer (Agilent). Dual indexed Illumina libraries were prepared from cDNA using a reduced volume NexteraXT reaction (1:12) on the Mosquito HV (Hendricks et al., in preparation). Final libraries were quantified using picogreen and spot-checked on the Fragment Analyzer before pooling and final quantification using qPCR on a Roche LC480II.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
NextSeq 500 sequencing using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Gene expression was quantified using RSEM version 1.3.0 and STAR version 2.5.3a alignment to a transcriptome derived from the human BDGP6 primary assembly and a version 92 annotation.
Assembly: BDGP6 Drosophila melanogaster assembly with version 92 annotation
Supplementary files format and content: 1b1sm_isoform_intCt.txt.gz is a tab delimited text file of isoform counts
Supplementary files format and content: 1b1sm_isoform_l2tpm.txt.gz is a tab delimited text file of isoform l2tpm vaules
Supplementary files format and content: 1b1sm_l2tpm.txt.gz is a tab delimited text file of gene l2tpm vaules
Supplementary files format and content: 1b1sm_intCt.txt.gz is a tab delimited text file of gene counts
|
| |
|
| Submission date |
Jan 16, 2023 |
| Last update date |
Feb 08, 2023 |
| Contact name |
Charles Arthur Whittaker |
| E-mail(s) |
[email protected]
|
| Organization name |
Koch Institute
|
| Street address |
77 Mass Ave 76-189
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02152 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE222976 |
Molecular Logic of Synaptic Diversity Between Drosophila Tonic and Phasic Motoneurons |
|
| Relations |
| BioSample |
SAMN32756783 |
| SRA |
SRX19045840 |
