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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 22, 2017 |
| Title |
P20_XY_Meioc_wild_type_RIP-input-RNA-seq_1 |
| Sample type |
SRA |
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| Source name |
postnatal testis
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: testis
Stage: P20
genotype: wild-type
preclearing: yes
rip antibody: none
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RIP-seq experiments, RNA was precleared with Dynabeads (ThermoFisher Scientific), immunoprecipitated, and isolated via phenol/chloroform extraction.
For RIP-seq experiments, Clontech SMARTer Stranded RNA-Seq Kit with rRNA depeletion was used accorindg to the manufacturer's recommendations.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
YTHDC2-RIP_sample_5
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| Data processing |
Sequenced reads were mapped to mm10 using Tophat with parameter -g1
FPKMs were calculated using Cufflinks
For RIP-seq data, counts were obtained from HTSeq and normalized via DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Cufflinks output, counts from HTSeq, or normalized counts from DESeq2
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| Submission date |
Nov 30, 2016 |
| Last update date |
Apr 08, 2024 |
| Contact name |
Maria M. Mikedis |
| E-mail(s) |
maria.mikedis@cchmc.org
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| Organization name |
Cincinnati Children's Hospital Medical Center
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| Street address |
240 Albert Sabin Way
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (2) |
| GSE90702 |
Identification of the embryonic germ cell Meioc-/- transcriptome, MEIOC targets in postnatal testis, and YTHDC2 targets in postnatal testis in mouse |
| GSE96921 |
Identification of YTHDC2 targets in mouse postnatal testis |
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| Relations |
| BioSample |
SAMN06076931 |
| SRA |
SRX2694316 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2410953_MM123-1c_DESeq2_normalized.counts.txt.gz |
102.4 Kb |
(ftp)(http) |
TXT |
| GSM2410953_MM123-1c_HTSeq_counts.txt.gz |
83.2 Kb |
(ftp)(http) |
TXT |
| GSM2410953_MM123-1c_genes.fpkm_table.txt.gz |
128.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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