|
Status |
Public on Jul 27, 2023 |
Title |
PRO_72h_Bioreplicate 2 |
Sample type |
SRA |
|
|
Source name |
8 hour hatching blastula embryos
|
Organism |
Strongylocentrotus purpuratus |
Characteristics |
tissue: 8 hour hatching blastula embryos genotype: Wild
|
Growth protocol |
15 degrees Celsius
|
Extracted molecule |
total RNA |
Extraction protocol |
Density gradient nuclear prep (Arenas-Mena et. al, 2021) https://doi.org/10.1186/s12864-021-07936-0 PRO-seq (Arenas-Mena et. al, 2021) https://doi.org/10.1186/s12864-021-07936-0. Quick PRO-seq (Judd et. al, 2020) https://www.protocols.io/view/a-rapid-sensitive-scalable-method-for-precision-ru-57dg9i6.pdf
|
|
|
Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
PRO-seq 72h_5.0_minus3.rpm.bw 72h_5.0_plus3.rpm.bw 72h_5.0_3_.dREG.peak.prob_100_merged_sort.bed
|
Data processing |
Read map and data processing as in (Arenas-Mena et. al, 2021) Assembly: Sp5.0 https://www.ncbi.nlm.nih.gov/assembly/GCF_000002235.5/ Library strategy: PRO-seq and Quick-PRO-seq
|
|
|
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) |
GSE234140 |
Accessibility and activity of transcriptional regulatory elements during sea urchin embryogenesis and differentiation [PRO-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 |
SAMN35622287 |
SRA |
SRX20593407 |