Zhang_Cell2024_WT_forward

Description

RNA-seq datasets of BJ fibroblasts with indicated genetic modifications (TMEM2-OE, or TMEM2-OE TGFBR1-KO) and/or pharmaceutical treatments (1 ng/mL TGF-β1 treatment for 24 hours). Four replicates per condition.

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Cells were grown to 80% of confluency followed by RNA purification using an RNeasy Mini Kit (74106, Qiagen) and stored at -80 °C. Four biological replications were included for each treatment. For Figure 5E, RNA-Seq library preparation was performed using Roche products, KAPA mRNA HyperPrep Kit, and KAPA Unique Dual Index Adapters. NanoDrop and Qubit instruments (Thermo Fisher) were used to measure nucleic acid concentrations. Agilent BioAnalyzer was used to determine the quality of pre-library total RNA and the library. Single direction sequencing was performed using an Illumina NovaSeq, mode S1, SR100 at the Vincent J. Coates Genomic Sequencing Core at University of California, Berkeley. For Figure 3E, 6A/B, and S4E/F, RNASeq library preparation was performed using TruSeq RNA Library Prep kit and Adapter sequences by Azenta. Paired end sequencing was performed on the Illumina NovaSeqX instrument by Azenta. RNA-Seq analysis was performed by uploading .fastq files to the Galaxy web platform, using the public server at usegalaxy.org. and human FASTA reference transcriptome Homo_sapiens.GRCh38.cdna.all.fa, downloaded from ensembl. Tools included Kallisto Quant v0.46.2+galaxy and DESeq2, v2.11.40.7+galaxy2. 1,2

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