|
| Status |
Public on Mar 16, 2018 |
| Title |
Drosophila nuclei sci-ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Nuclei isolated from whole embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole embryos
developmental stage: 2 to 4 hours after egg laying
developmental stage: 6 to 8 hours after egg laying
developmental stage: 10 to 12 hours after egg laying
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole embryos were fixed and nuclei were isolated (please see publication for more details).
Please see publication for details on library construction.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Accessible genomic DNA
|
| Data processing |
BCL files were converted to fastq format with bcl2fastq v2.16.
Barcode sequences were corrected to expected barcodes with custom python script.
Reads were trimmed (for adapter read-through) with Trimmomatic v0.32.
Reads were mapped to dm3 with bowtie v2.2.3.
Reads not mapping to the assembled nuclear chromsomes, as well as reads with invalid cell barcodes, were filtered using samtools v1.1 and grep.
Duplicate reads from each cell were filtered out with a custom python script.
Filtered out barcodes with few reads using custom R script.
Mapped reads to 2kb windows in the genome using custom python script.
After clustering cells, called peaks on clusters of cells using MACS2 v2.1.1.20160309.
Overlapped reads with summits of accessibility using custom python script.
Genome_build: dm3
Supplementary_files_format_and_content: ".2kbmatrix.txt.gz": Multiple column tab-separated vector - first 4 columns contain location information for each 2kb window, remaining columns include counts of reads overlapping that site assigned to each barcode.
Supplementary_files_format_and_content: ".summitmatrix.txt.gz": Multiple column tab-separated vector - first 4 columns contain location information for each hypersensitivity summit, remaining columns include counts of reads overlapping that site for each cell barcode.
Supplementary_files_format_and_content: ".indextable.txt": 2 column tab-separated vector - Column 1 = list of valid barcode combinations included in experiment; Column2 = developmental stage of embryos and PCR plate that barcode represents.
|
| |
|
| Submission date |
Jul 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Darren A. Cusanovich |
| E-mail(s) |
darrenc@arizona.edu
|
| Organization name |
University of Arizona
|
| Department |
Cellular and Molecular Medicine
|
| Street address |
1230 N Cherry Avenue, BSRL 421
|
| City |
Tucson |
| State/province |
AZ |
| ZIP/Postal code |
85721 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE101581 |
The cis-regulatory dynamics of embryonic development at single cell resolution |
|
| Relations |
| BioSample |
SAMN07362069 |
| SRA |
SRX3014178 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2706365_10to12.2kbmatrix.txt.gz |
44.9 Mb |
(ftp)(http) |
TXT |
| GSM2706365_10to12.indextable.txt.gz |
107.0 Kb |
(ftp)(http) |
TXT |
| GSM2706365_10to12.summitmatrix.txt.gz |
31.1 Mb |
(ftp)(http) |
TXT |
| GSM2706365_2to4.2kbmatrix.txt.gz |
62.8 Mb |
(ftp)(http) |
TXT |
| GSM2706365_2to4.indextable.txt.gz |
110.0 Kb |
(ftp)(http) |
TXT |
| GSM2706365_2to4.summitmatrix.txt.gz |
37.1 Mb |
(ftp)(http) |
TXT |
| GSM2706365_6to8.2kbmatrix.txt.gz |
60.9 Mb |
(ftp)(http) |
TXT |
| GSM2706365_6to8.indextable.txt.gz |
110.2 Kb |
(ftp)(http) |
TXT |
| GSM2706365_6to8.summitmatrix.txt.gz |
40.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
