|
| Status |
Public on Jan 01, 2019 |
| Title |
iR2ko_355 |
| Sample type |
SRA |
| |
|
| Source name |
total kidney
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Rhbdf2-/-
age: 7-9 months
Sex: Female
tissue: Kidney
|
| Treatment protocol |
Female littermates (WT, Rhbdf2-/-, Fcgr2b-/-, Fcgr2b-/-Rhbdf2-/- mice) were aged to 7-9 m of age.
|
| Growth protocol |
C57BL/6 female mice (The Jackson Laboratory) were maintained in the Hospital for Special Surgery and Weill Cornell Animal Facility in full compliance with guidelines approved by the Institutional Animal Care and Use Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1. For RNA-sequencing in whole kidneys, total RNA was extracted from whole kidneys from well-perfused mice using an RNeasy mini kit (Qiagen).
2. For sorted macrophages, kidneys from 7-9 m old mice were first minced and digested with collagenase B (Roche) for 45 minutes at 37ºC. Macrophages were enriched by centrifuging cells in 40% percoll/PBS (v/v). Cells were stained with fluorochrome-conjugated anti-mouse antibodies, and CD45+F4/80hiCD11b+Ly6G-Ly6C- kidney macrophages were sorted into RLT lysis buffer directly. Total RNA was extracted using an RNeasy mini kit (Qiagen).
1. For total kidney, library preparation and sequencing were performed by Genomics Resources Core Facility at Weill Cornell Medical College using TruSeq RNA library prep kit (Illumina) followed by single read sequencing on the Illumina HiSeq 2500 instrument (4-6 samples/SR lane, 50 bp reads).
2. For sorted macrophages, library preparation and sequencing were performed at Epigenetics Core facility at Weill Cornell Medical College using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) followed by single read clustering and 51 cycles sequencing on the Illumina HiSeq 2500 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sorting strategy: Total tissue
PolyA-enriched RNA
08_iR2ko_355_AGTTCC_L006_R1
Processed data file: total_kidney_edgeR_2016_07_06_submitted.csv
|
| Data processing |
1. 51 bp reads were aligned to annotated mouse genome (mm10, build 38.75, 41,128 genes and 87,108 transcripts) using CLC Bio Genomic Workbench 7.5 (Qiagen).
2. Unique exon reads were used as an expression metric. Genes with less than 3 counts per million (cpm) in all replicates were considered non-expressing and filtered out prior to differential expression analysis.
3. The feature counts were normalized to the library size using the weighted trimmed mean of M-values methods.
4. A quasi-likelihood negative binomial generalized log-linear model was fit to read counts for each gene. An empirical Bayes quasi-likelihood F-tests likelihood ratio tests was performed gene-wise to evaluate the significance of differences in expression between analyzed groups Genes with a Benjamini-Hochberg false discovery rate (FDR)-corrected p-value < 0.01 and at least two-fold expression change were considered to be differentially expressed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *csv: Comma-separated text files include differentially expressed genes.
|
| |
|
| Submission date |
Dec 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yurii Chinenov |
| Organization name |
Hospital for special surgery
|
| Department |
Research Division
|
| Lab |
HSS Genomics Center
|
| Street address |
535 E 71 str, Hospital for Special Surgery
|
| City |
New york |
| State/province |
New York |
| ZIP/Postal code |
11361 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE107705 |
iRhom2 Promotes Lupus Nephritis through ADAM17-Dependent TNF-α and EGFR Signaling |
|
| Relations |
| BioSample |
SAMN08133519 |
| SRA |
SRX3445305 |
