|
| Status |
Public on Feb 04, 2022 |
| Title |
A1 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Col4a3-/-
tissue: kidney
strain: 129SJ x C57Bl/6J
treatment: PBS QW
group name: Veh
|
| Treatment protocol |
Col4a3-/- mice were treated from 5 weeks of age with weekly (QW) Sub-Cutaneous injection of PBS (Vehicle), Lademirsen at 50mg/kg in PBS (Anti-miR-21) or ramipril at 11 mg/L ad libitum in drinking water (ACEi) and sacrificed at 15 weeks of age. Wild type mice (WT) did not receive any treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by TRIzol and chloroform extraction from homogenized adipose tissue followed by RNeasy purification to remove genomic DNA (Qiagen).
RNA-seq of total RNA samples was conducted on the Illumina HiSeq 2000 platform, producing 100bp paired-end reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
FCH5V5HBBXX-HKMUSfrpEAAARABPEI-218_L5
|
| Data processing |
Using Array Studio version 9.0 (Omicsoft Corporation, a Qiagen Company), reads were filtered according to the following protocol: Trimming /Mode=TrimByQuality /ReadTrimQuality=20; FilterSource IlluminaAdapters,Ercc /CustomFile=""; Options /FileFormat=AUTO /QualityEncoding=Automatic /WriteFilterFiles=False /EnableLengthCutoff=True /LengthCutoff=25 /EnableMaxQualityCutoff=False /MaxQualityCutoff=15 /EnableAverageQualityCutoff=True /AverageQualityCutoff=15 /EnablePolyRateCutoff=True /PolyRateCutoff=75 /OutputFolder="/site/ne/data/bi/omicsoft/FtpRootCR/Users/soka01/wax.1055_test/wax1057_test" /CompressionMethod=Gzip /Gzip=True /PairedEnd=True /FilterPairByBothEnds=True /ParallelJobNumber=32; End;
Using Array Studio version 9.0 Mapping to the reference was as follows: Reference Mouse.B38; GeneModel Ensembl.R83; Trimming /Mode=TrimByQuality /ReadTrimQuality=20; Options /ParallelJobNumber=32 /PairedEnd=True /FileFormat=AUTO /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=True /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /OutputFolder="/site/ne/data/bi/omicsoft/FtpRootCR/Users/soka01/Alport_kidney_RNAseq/Study13-04182_April2016/B38_R83_mapped" /ThreadNumber=8 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=200 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=True /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False; Output Alport kidney 4.16; End;
Using Array Studio version 9.0 counts & FPKM values were generated using the following parameters: Begin ReportGeneTranscriptCounts /Namespace=NgsLib /RunOnServer=True; Project alport.kidney.study13-04182; Data "alport.kidney.study13-04182.exu09sep2016.ricbr01\\Alport kidney 4.16"; GeneModel Ensembl.R83; Options /ExpressionMeasurement=RPKM+Count /ParallelJobNumber=32 /Add1=False /CountFragments=True /ExcludeMultiReads=False /UseEffectiveTranscriptLength=False /CountStrandedReads=True /CountReverseStrandedReads=True /AutoTrimUtr=False /OutputFolder="/site/ne/data/bi/omicsoft/FtpRootCR/Users/soka01/Alport_kidney_RNAseq/Study13-04182_April2016/B38_R83_mapped"; Output alport kidney 4.16; End;
Using Array Studio version 9.0.1.38 transcripts were filtered based on counts as follows: By Variable; Filter Sum>=0.1; Options /Group=(all) /ApplyToAllGroups=True /CountingCutoff=5 /FilterByDetection=False; Output counts_greaterthan0.1; End; End;
Using Array Studio version 9.0.1.38, normalized FPKM values were transformed as follows: Data alport.kidney.study13-04182\\alport kidney 4.16.FPKM /Variables=alport.kidney.study13-04182\\counts_greaterthan0.1; By Observation; Options /Normalization=ScaleQuantile /Parameter1=75 /Parameter2=10; Output filteredFPKM_ScaleQuantNorm; End;
Using Array Studio version 9.0.1.20 expression data were log transformed as follows: Data alport.kidney.study13-04182\\alport kidney 4.16.FPKM; Options /Transformation=Log2 /Add=1; Output alport kidney 4.16_log2FPKM; End;
Genome_build: Omicsoft Mouse.B38
|
| |
|
| Submission date |
Jul 12, 2021 |
| Last update date |
Feb 04, 2022 |
| Contact name |
herve husson |
| E-mail(s) |
herve.husson@gmail.com
|
| Phone |
6172578094
|
| Organization name |
Sanofi
|
| Department |
genomics medicine unit
|
| Street address |
49 New York Avenue
|
| City |
Framingham |
| State/province |
ma |
| ZIP/Postal code |
01701 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE179938 |
Anti-microRNA-21 therapy on top of ACE-inhibition delays renal failure in Alport syndrome mouse models |
|
| Relations |
| BioSample |
SAMN20172699 |
| SRA |
SRX11412346 |
