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Sample GSM7728773

Query DataSets for GSM7728773

Status

Public on Jul 18, 2024

Title

PDX-G266, Vehicle, LWHR35

Sample type

SRA

Source name

PDX-G266 mice, a model of CRPC

Organism

Homo sapiens

Characteristics

disease state: castration-resistant prostate cancer (CRPC)
tissue: PDX-G266
treatment: Vehicle

Extracted molecule

polyA RNA

Extraction protocol

P2830 : RNA-Seq libraries were generated according to manufacturer's instructions from 300 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94oC for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 13 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Reads preprocessing steps were performed using cutadapt 1.10, reads were mapped onto the hg38 assembly of Homo sapiens genome using STAR version 2.5.3a. Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 108 and “union” mode. Only non-ambiguously assigned reads were retained for further analyses. Read counts were normalized across libraries by published method
Assembly: hg38
Supplementary files format and content: alldata_count.tsv

Submission date

Aug 22, 2023

Last update date

Jul 18, 2024

Contact name

Gilles Laverny

E-mail(s)

laverny@igbmc.fr

Organization name

IGBMC

Street address

1 rue Laurent Fries