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| Status |
Public on Feb 05, 2024 |
| Title |
mESCs NELFb, 3 -- S/L |
| Sample type |
SRA |
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| Source name |
Mouse mESCs
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| Organism |
Mus musculus |
| Characteristics |
assay: PRO-seq
degron type: NELFb-dTAG
dtag-13 treatment: untreated
heat shock: no
replicate: 3
media used to grow the cells: serum lift (S/L)
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction, run-on, and library preparation were executed according to “Mahat, D. B. et al. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat. Protoc. 11, 1455–1476 (2016).” (PMID: 27442863).
Library prep was performed using Illumina custom adapters: Reverse 3' RNA adapter (/5Phos/NNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT) and Reverse 5' RNA Adapter (5'-CCUUGGCACCCGAGAAUUCCA-3').
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
FASTQ data was aligned and processed using the proseq2.0 pipeline developed by Danko lab (https://github.com/Danko-Lab/proseq2.0).
The mESC data was competitively aligned to a merged genome assembly of mm10 and dm3. Merging the two genome builds was performed using fastq merge.
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| Submission date |
Jan 28, 2023 |
| Last update date |
Sep 04, 2025 |
| Contact name |
Brent Basso |
| E-mail(s) |
bab364@cornell.edu
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| Organization name |
Cornell University
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| Department |
Computational Biology
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| Lab |
Danko/Lis
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| Street address |
1631 Dryden Rd.
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| City |
Freeville |
| State/province |
NEW YORK |
| ZIP/Postal code |
13068 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE223913 |
Pol II pausing is a milestone on the road to complex animals |
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| Relations |
| BioSample |
SAMN32949454 |
| SRA |
SRX19205934 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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