|
| Status |
Public on Feb 04, 2019 |
| Title |
WT_Sample 4 |
| Sample type |
SRA |
| |
|
| Source name |
WT
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
gender: female
age: 16w
genotype/variation: wild type
cell type: Alveolar macrophage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy micro kit (Qiagen).
cDNA were prepared from 100 pg of total RNA per sample using SMARTer Ultra Low Input RNA Kit for Sequencing-v3 (Clontech Laboratories) following the standard protocol with slight modification (18 PCR cycles). The cDNA was fragmented using Covaris S2 Focused-ultrasonicator (Covaris) and RNA-seq libraries were prepared from the fragmented cDNA with Ovation Ultralow DR Multiplex system V2 (Nugen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Trimming; FASTX Toolkit 0.0.14, fastx_trimmer -f 5
Mapping; bowtie 1.1.2, bowtie -p 2 -aS -X 800 --offrate 1
Expression quantitative detarmination; eXpress 1.5.1, express
Production of matrix data file for express output data (only fpkm)
Genome_build: RefSeq (downloaded in 20150626)
Supplementary_files_format_and_content: csv
|
| |
|
| Submission date |
Mar 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kazuhiko Igarashi |
| E-mail(s) |
igarashi@med.tohoku.ac.jp
|
| Phone |
+81227177597
|
| Organization name |
Tohoku University
|
| Street address |
Seiryo 2-1
|
| City |
Sendai |
| ZIP/Postal code |
980-8575 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE79558 |
Bach2 keeps homeostasis in lung by regulating inflammatory response and maintaining function of alveolar macrophage. |
|
| Relations |
| BioSample |
SAMN04577671 |
| SRA |
SRX1658958 |
