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Sample GSM4132288 Query DataSets for GSM4132288
Status Public on Nov 15, 2019
Title First instar larval brain cells, Starvation condition (scRNAseq) 3 - sample 7
Sample type SRA
 
Source name Brain cells
Organism Drosophila melanogaster
Characteristics strain: Wild type CS
development stage: First instar larval
tissue: brain
stress: starvation
Treatment protocol Larvae were collected at 11 ALH, quickly washed to remove food leftovers and transferred to a Petri dish with 2% of agar, humidified with PBS, for 4 hours at 25 °C.
Growth protocol All flies were kept at 25°C in a 12h/12h light-dark cycle in vials containing conventional cornmeal agar medium
Extracted molecule total RNA
Extraction protocol Dissected brains in PBS were dissociated into single-cell suspensions by an enzimatic treatment with collagenase. mRNAs were obtained by applying 10X Genomics protocol for scRNAseq, Chromium Single Cell 3’ Library & Gel Bead Kit v2.
Libraries were constructed accoring to the manufacturer's guideline, for sequencing on a Illumina NovaSeq 6000
Libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Sample 7
Data processing Sequenced libraries with processed with cell ranger pipeline (10X Genomics)
Each time, cell ranger count ran with the specific expected number of cells to recover.
Single datasets were later aggregated with cell ranger aggr pipeline.
Genome_build: The reference genome was built based on the 3rd 2018 FlyBase release (D. melanogaster r6.22)
Supplementary_files_format_and_content: Matrix files originated with cell ranger aggr pipeline
 
Submission date Oct 21, 2019
Last update date May 14, 2020
Contact name Simon Sprecher
E-mail(s) simon.sprecher@unifr.ch
Organization name University of Fribourg
Department Biology
Lab Sprecher Lab
Street address Chemin du Musée 10
City Fribourg
State/province Fribourg
ZIP/Postal code 1700
Country Switzerland
 
Platform ID GPL25244
Series (1)
GSE134722 Single cell transcriptome atlas of the Drosophila larval brain
Relations
BioSample SAMN13068321
SRA SRX7028155

Supplementary file Size Download File type/resource
GSM4132288_FirstInstarLarvalBrainStarvationCondition_sample7_10X_barcodes.tsv.gz 4.9 Kb (ftp)(http) TSV
GSM4132288_FirstInstarLarvalBrainStarvationCondition_sample7_10X_genes.tsv.gz 129.1 Kb (ftp)(http) TSV
GSM4132288_FirstInstarLarvalBrainStarvationCondition_sample7_10X_matrix.mtx.gz 5.4 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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