|
| Status |
Public on May 15, 2023 |
| Title |
cSiah1a/2f/f::CD11ccre alveolar macrophage, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell type: alveolar macrophage
genotype: cSiah1a/2f/f::CD11ccre
|
| 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 |
Cd11c_rep1
|
| 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 |
SAMN31318058 |
| SRA |
SRX17916148 |
