RNA-Seq of HeLa-S3 - SRA

SRX22913307: RNA-Seq of HeLa-S3
1 ILLUMINA (Illumina NovaSeq 6000) run: 40.5M spots, 12.1G bases, 3.8Gb downloads

Design: The RNA sample preparations involved using 0.4 g of RNA per sample with the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturers guidelines, incorporating index codes for sample attribution. Initially, mRNA purification was executed using poly-T oligo-attached magnetic beads, followed by fragmentation in NEBNext First Strand Synthesis Reaction Buffer (5X) under increased temperature with divalent cations. First strand cDNA synthesis was conducted with random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-), followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Blunt ends were generated from remaining overhangs through exonuclease/polymerase activities. Adenylation of DNA fragment ends preceded ligation with NEBNext Adaptors featuring a hairpin loop structure for hybridization preparation. Selection of cDNA fragments, preferably 250~300 bp, was achieved via purification using the AMPure XP system (Beckman Coulter, Beverly, USA). Subsequent PCR employed Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. The resulting PCR products underwent purification with the AMPure XP system, and library quality was assessed using the Agilent Bioanalyzer 2100 system.

Submitted by: Sabanci University

Study: Dynamics of UV-induced changes and regulations in 3D genome organization

PRJNA1053630 • SRP478417 • All experiments • All runs

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The goal is to understand the effects of UV-exposure on the 3D genome architecture and transcriptional regulation. Accordingly, HeLa-S3 cells were cultured and exposed to 254-nm UV (1 J/m2/s) for 20 seconds. At the recovery time points of 12, 30 and 60 minutes post-UV, cells were harvested. A non-UV control group has been processed as well. Hi-C, and RNA-Seq techniques have been applied.

Sample: RNA-Seq,non-UV,rep2

SAMN38862438 • SRS19881905 • All experiments • All runs

Organism: Homo sapiens

Library:

Name: rna_0_2

Instrument: Illumina NovaSeq 6000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: Oligo-dT

Layout: PAIRED

Runs: 1 run, 40.5M spots, 12.1G bases, 3.8Gb

Run	# of Spots	# of Bases	Size	Published
SRR27234817	40,498,873	12.1G	3.8Gb	2024-05-27

ID:: 30975897

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