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Sample GSM7000686 Query DataSets for GSM7000686
Status Public on Feb 05, 2024
Title mESCs NELFb, 28 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG
Sample type SRA
 
Source name Mouse mESCs
Organism Mus musculus
Characteristics assay: PRO-seq
degron type: NELFb-dTAG
dtag-13 treatment: 60min dTAG
heat shock: yes
replicate: 1
media used to grow the cells: serum lift (S/L)
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').
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
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.
 
Submission date Jan 28, 2023
Last update date Feb 05, 2024
Contact name Alexandra Georgiana Chivu
E-mail(s) agc94@cornell.edu
Phone 6072624972
Organization name Cornell University
Department Molecular Biology and Genetics
Lab Danko and Lis labs
Street address 215 Tower Rd
City Ithaca
State/province NY
ZIP/Postal code 14853
Country USA
 
Platform ID GPL19057
Series (1)
GSE223913 Pol II pausing is a milestone on the road to complex animals
Relations
BioSample SAMN32949447
SRA SRX19205941

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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