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| Status |
Public on Jun 03, 2021 |
| Title |
PRO-seq_20h_SE_Biorep1_Tech_2 |
| Sample type |
SRA |
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| Source name |
20 hour hatching blastula embryos
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| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
tissue: embryo
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| Growth protocol |
15 degrees Celsius
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| Extracted molecule |
total RNA |
| Extraction protocol |
Density gradient nuclear prep
Chu et al., 2018. PMCID: PMC6204104
PRO-seq
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
proseq2.0 default parameters https://github.com/Danko-Lab/proseq2.0
Genome_build: Sp3.1
Supplementary_files_format_and_content: 20h_TOTAL_Sep2020_plus3.rpm.bw and 20h_TOTAL_Sep2020_minus3.rpm.bw, bigwig files for the combinned signal from all replicates
Supplementary_files_format_and_content: 20hTOTAL_sep2020.dREG.peak.prob.bed.gz, bed file dREG predictions based on the total signal from all replicates
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| Submission date |
Oct 29, 2020 |
| Last update date |
Jun 09, 2023 |
| Contact name |
Cesar Arenas-Mena |
| E-mail(s) |
cesar.arenasmena@csi.cuny.edu
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| Organization name |
CSI CUNY
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| Department |
Biology
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| Street address |
2800 Victory Boulevard
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| City |
Staten Island |
| State/province |
New York |
| ZIP/Postal code |
10314 |
| Country |
USA |
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| Platform ID |
GPL20965 |
| Series (2) |
| GSE160460 |
PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (PRO-Seq) |
| GSE160463 |
PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos |
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| Relations |
| Reanalyzed by |
GSM7472524 |
| BioSample |
SAMN16597512 |
| SRA |
SRX9402640 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4873700_Sea_Urchin_Embryos_20_hours_dedup_QC_end_minus3.rpm.bw |
3.8 Mb |
(ftp)(http) |
BW |
| GSM4873700_Sea_Urchin_Embryos_20_hours_dedup_QC_end_plus3.rpm.bw |
3.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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