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| Status |
Public on Dec 31, 2023 |
| Title |
kidney, PND7, mCherry Glis3 KO, rep5 |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
age: PND7
genotype: mCherry Glis3 KO
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| Extracted molecule |
total RNA |
| Extraction protocol |
Purelink RNA mini kit was used for RNA extraction
RNA libraries were prepared using TruSeq RNA library preparation kit from Illumina following manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Read pairs were filtered to retain only those with mean base quality scores at least 20, then aligned via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Counts per gene were determined via featureCounts (Subread v1.5.0-p1) with parameters "-s0 -Sfr -p" for the unstranded PAX8-cre dataset and "-s2 -Sfr -p" for the reverse-stranded mCherry dataset.
Depth tracks were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand {Unstranded,Stranded} --outWigNorm RPM", followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: counts-per-gene matrix per dataset (tab-delimited text)
Supplementary files format and content: normalized depth tracks (bigWig)
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| Submission date |
Aug 04, 2023 |
| Last update date |
Dec 31, 2023 |
| Contact name |
Hong Soon Kang |
| E-mail(s) |
kang1@niehs.nih.gov
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| Phone |
984-287-3921
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| Organization name |
NIH/NIEHS
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| Department |
IIDL
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| Lab |
Cell Biology Group
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| Street address |
111 T.W. Alexander Dr.
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| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE240071 |
Regulation of gene expression by GLIS3 during neonatal kidney development |
| GSE240074 |
GLIS3 |
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| Relations |
| BioSample |
SAMN36836704 |
| SRA |
SRX21247538 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7680859_mCherry-P7-KO-rep5.depthRPM.minus.bigWig |
144.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM7680859_mCherry-P7-KO-rep5.depthRPM.plus.bigWig |
147.4 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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