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Sample GSM6936362

Query DataSets for GSM6936362

Status

Public on Feb 08, 2023

Title

M1 muscle cell, segment A4, animal 5, cell d306040

Sample type

SRA

Source name

muscle cell

Organism

Drosophila melanogaster

Characteristics

tissue: muscle cell
segment: A4
cell type: M1
animal: 5
gender: M
strain: w[1118]
genotype: w[1118]

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