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Sample GSM6647484 Query DataSets for GSM6647484
Status Public on May 15, 2023
Title cSiah1a/2f/f::Lyz2cre alveolar macrophage, replicate 3
Sample type SRA
 
Source name lung
Organism Mus musculus
Characteristics tissue: lung
cell type: alveolar macrophage
genotype: cSiah1a/2f/f::Lyz2cre
Extracted molecule total RNA
Extraction protocol PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module.
Barcoded libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (NEB, Ipswich MA). Libraries were pooled and sequenced single-end (1X75) on an Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description LyzS_rep3
Data processing Illumina Truseq adapters and polyA/polyT sequences were trimmed from raw reads using Cutadapt version 2.3.
Trimmed reads were aligned to mouse genome version mm10 and Ensembl gene annotations version 84 using STAR version 2.7.0d_0221 adopting alignment parameters from ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline).
RSEM version 1.3.1 was used to obtain gene level estimated counts and transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes TPM (Transcripts Per Million) values for each sample.
 
Submission date Oct 17, 2022
Last update date May 15, 2023
Contact name Ze'ev A. Ronai
E-mail(s) ronai@sbpdiscovery.org
Organization name Sanford Burnham Prebys Medical Discovery Institute
Department Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center
Street address 10901 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL19057
Series (2)
GSE215920 Control of alveolar macrophage differentiation by Siah1a/2 ubiquitin ligases limits carcinogen-induced lung adenocarcinoma [Bulk RNA-seq]
GSE215993 Control of alveolar macrophage differentiation by Siah1a/2 ubiquitin ligases limits carcinogen-induced lung adenocarcinoma
Relations
BioSample SAMN31318059
SRA SRX17916147

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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