|
| Status |
Public on Apr 01, 2018 |
| Title |
Other, non-PMC cells isolated from 24 hpf embryos, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
24 hours post fertilization isolated non-PMC cells
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
developmental stage: 24 hours post fertilization
|
| Growth protocol |
S. purpuratus eggs fertilized and cultured in artificial sea water at 15 degrees Celcius
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted using lysis buffer washes and ATAC-seq was performed: 150,000 nuclei were digested with 2.5 ul Tn5 transposase and a Nextera library was created.
Nextera library kit used to generate Illumina sequencing library for NextSeq
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC-seq
PMC_Other_RPS.bed
|
| Data processing |
Adapter sequences were trimmed using Cutadapt (v1.9)
Reads were mapped to the S. purpuratus genome v 3.1 using Bowtie2 (v2.1.0) with default parameters
Bowtie2 SAM output format was converted to BAM format and PCR duplications were removed and read counts were equalized using Samtools v1.3
Bedtools (v2.19.1) was used to convert the BAM output into BED format.
Fseq (v1.85) was used to call peaks using parameters -f 0 and -t 2
The fraction of reads within peaks (the FRiP score) was calculated using Bedtools (v2.19.1) by extracting and counting all reads within peaks and dividing by the total number of reads mapped.
Separate reference peak sets (RPSs) were generated for the DNase-seq and ATAC- seq data by first identifying all replicate peaks that overlapped by at least 75% non-reciprocally and then merging all such peaks across samples separately for the DNase-seq or ATAC-seq data using Bedops (v2.4.2)
Read counts corresponding to peaks in the RPS were generated using HTSeq (v0.6.0)
Differential peaks were identified using DESeq2
Genome_build: Strongylocentrotus purpuratus genome version 3.1 (Spur_3.1)
Supplementary_files_format_and_content: BED files contain peaks called by Fseq (v1.85), and the reference peak set (RPS) generated by merging the peaks using Bedops(v2.4.2). .txt files contain read counts corresponding to the peaks in the RPS, generated by HTseq (v0.6.0).
|
| |
|
| Submission date |
Mar 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles A Ettensohn |
| E-mail(s) |
ettensohn@cmu.edu
|
| Organization name |
Carnegie Mellon University
|
| Street address |
4400 Fifth Avenue
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL23218 |
| Series (1) |
| GSE96927 |
Chromatin accessibility profiling identifies cis-regulatory modules in an early embryonic cell lineage |
|
| Relations |
| BioSample |
SAMN06628136 |
| SRA |
SRX2661971 |
