|
| Status |
Public on Dec 14, 2021 |
| Title |
bulkATAC-L1-40-2 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: brain
cell type: FACS-sorted L1 neurons
age: 40hAPF
genotype: wild type
|
| Growth protocol |
Maintenance and rearing of fly lines, as well as staging of pupae was done as described in Tan et al 2015
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
FACS-sorted cell suspension
Single cell RNA-seq: FACS-sorted cell suspension were loaded on 10X Genomics Chromium machine for single cell prepration. Single-cell RNA-Seq libraries were generated using Chromium Single Cell Reagent Kit V3 according to the manufacturer's protocol. Bulk RNA-seq: FACS sorted cell suspension were used for library prepration with SMART-seq2 protocol published by Picelli et al, 2014. Bulk ATAC-seq: FACS sorted cell suspension were used to library prep with modified protocol published by Buenrostro et al., 2013
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
L1 bulk ATAC-seq peak level.xlsx
|
| Data processing |
bulk ATAC-seq: Raw fastq reads files were mapped to FlyBase reference genome (release 6.29) using Bowtie2 (2.2.9) and uniquely mapped genes were kept. All samples were pooled together prior to peak calling. Read start positions were shifted +4 or -5bp and used for peak calling using MACS2 (2.1.1) with parameters “-q 0.01 --nomodel --shift -100 --extsize 200”. Then bedtools multicov (2.27.1) was used to sum the total reads within each peak separately for each sample. Peaks with CPM ≥ 4 were used for counts normalization with edgeR.
bulk RNA-seq: fastq files were mapped to FlyBase reference genome (release 6.29) using STaR (2.6.0) and only uniquely mapped reads were collected. Genes with counts per million (CPM) ≥ 4 in more than 2 samples were used for normalization with R package edgeR (3.26.8). Gene expression was quantified using RPKM units (Reads Per Kilobase of exon per Million reads mapped), calculated based on reads in the sum of exons using customized scripts.
single cell RNA-seq: Fastq files were processed using Cell Ranger (3.1.0) pipeline using default parameters. Reference transcriptome package for Cell Ranger was generated using Drosophila melanogaster genome sequence and gene annotations from FlyBase (release 6.29). DGRP samples were demultiplexed based on parental genotypes using demuxlet (version 2).Downstream analysis including cell-type clustering was performed using Seurat package (3.1.2).
Genome_build: FlyBase 6.29
Supplementary_files_format_and_content: Bulk RNA-seq and bulk-ATAC-seq: abundance measurements in excel sheets; single cell RNA: cell-type cluster and counts in Seurat object.
|
| |
|
| Submission date |
Dec 11, 2021 |
| Last update date |
Dec 14, 2021 |
| Contact name |
Ying Lin |
| Organization name |
University of California, Los Angeles
|
| Street address |
675 Charles E. Young Drive South
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21306 |
| Series (1) |
| GSE190714 |
A global timing mechanism regulates cell-type specific wiring programs |
|
| Relations |
| BioSample |
SAMN23928651 |
| SRA |
SRX13386236 |
