 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 16, 2021 |
| Title |
Lung_WT_rep2 [AG56i_lung_WT] |
| Sample type |
SRA |
| |
|
| Source name |
Lung_WT
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wildtype
age: 15 weeks old
treatment: tamoxifen injected mice
tissue: Lung
|
| Treatment protocol |
5 week old mice received 3 i.p. injections of 50 μg/g tamoxifen during first week, RNA from tisues was isolated from 15 week old mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were collected and washed twice in ice-cold PBS and were maintained for 30min in RNA laterTM solution (Invitrogen). Next, tissues were transferred to RNAeasy plus lysis buffer (Qiagen)+ Bmercaptoethanol (AppliChem) and and snap-frozen on dry ice. Tissues were homogenized using Fast Prep-24 disruptor (MP) and the RNA isolated according to Qiagen RNeasy Plus Mini Kit (Qiagen) instruction manual. RNA concentration and quality were verified using 2100 Bioanalyzer (Agilent).
RNA-seq libraries were prepared from 500 ng of total RNA. RNA sequencing library preparation used Truseq Stranded RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA).
Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA). After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were 2x150 single-end sequencing using HiSeq 4000 SR, each sample being sequenced on three separate lanes to increase coverage per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
processed data file: Loyola_Foxc2_RNAseq_lung_counts.csv
|
| Data processing |
Illumina bcl2fastq v. 2.17
Each library was sequenced on three lanes. The 3 fastq files of each sample were concatenated, and read alignment and count summarization were performed using the bcbio-nextgen pipeline (v.19.03)
Reads were aligned using HISAT v. 2.1.0, and counts per gene were summarized using featureCounts of the Subread package v.1.6.3
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values file of counts per gene generated by featureCounts. Gene symbols are contained in the first column. The counts of the lung and the mesentery samples are contained in two separate files. Sample names contain indication of the genotype of each sample (WT=wildtype, KO=Foxc2 LEC KO)
|
| |
|
| Submission date |
Aug 17, 2020 |
| Last update date |
Jul 16, 2021 |
| Contact name |
Tania Wyss |
| Organization name |
Swiss Institute of Bioinformatics
|
| Street address |
Rue du Bugnon 25A
|
| City |
Lausanne |
| ZIP/Postal code |
1005 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE156319 |
Transcriptomes of adult mesentery and lung tissues from wildtype and Foxc2lecKO mice |
| GSE156320 |
FOXC2 controls adult lymphatic endothelial specialization, function and gut lymphatic barrier preventing multi-organ failure |
|
| Relations |
| BioSample |
SAMN15831191 |
| SRA |
SRX8955193 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
