|
| Status |
Public on Jul 27, 2023 |
| Title |
ATAC_RedSn_Bioreplicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Red Spherule Cells
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
tissue: Red Spherule Cells
genotype: Wild
|
| Growth protocol |
15 degrees Celsius
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear preps, ATAC-seq in embryos and larvae followed previously stablished protocols (Arenas-Mena et al., 2021) https://doi.org/10.1186/s12864-021-07936-0, except that for red spherule cells the lysis buffer during the nuclear prep was supplemented with 0.1 % NP40, 0.1% Tween-20, and 1% BSA, and the density gradient solutions were supplemented with 1% BSA to diminish nuclear shearing. Red spherule cells were purified from the coelomic fluid of adult sea urchins following a previously stablished method (Smith et al., 2019). OmniATAC in 72 hour embryos raised at 15 degrees C and red spherule cells was performed as previously described (Corces et al., 2017).
ATAC-seq (Arenas-Mena et. al, 2021) https://doi.org/10.1186/s12864-021-07936-0. Omni-ATAC protocol followed previously stablished protocol (Corces et. al, 2017) https://doi.org/10.1038/nmeth.4396
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC_RSCnB1_1_RSCnB2_1_merged_sort_RPM.bw
RSCn_B1_B2_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed
|
| Data processing |
ENCOCE-DCC atac-seq-pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) default parameters
MACS2 peak call p threshold set to 0.05.
Library normalization of merged biological replicates to reads per million (rpm).
Assembly: Sp5.0 https://www.ncbi.nlm.nih.gov/assembly/GCF_000002235.5/
|
| |
|
| Submission date |
Jun 05, 2023 |
| Last update date |
Jul 27, 2023 |
| Contact name |
Cesar Arenas-Mena |
| E-mail(s) |
cesar.arenasmena@csi.cuny.edu
|
| Organization name |
CSI CUNY
|
| Department |
Biology
|
| Street address |
2800 Victory Boulevard
|
| City |
Staten Island |
| State/province |
New York |
| ZIP/Postal code |
10314 |
| Country |
USA |
| |
|
| Platform ID |
GPL23218 |
| Series (2) |
| GSE234139 |
Accessibility and activity of transcriptional regulatory elements during sea urchin embryogenesis and differentiation [ATAC-seq] |
| GSE234143 |
Widespread priming of transcriptional regulatory elements by incipient accessibility or Pol II pause in early embryos of the sea urchin Strongylocentrotus purpuratus |
|
| Relations |
| BioSample |
SAMN35622319 |
| SRA |
SRX20593493 |
