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| Status |
Public on Aug 28, 2024 |
| Title |
RNA_FL_timecourse_E10.5+DMSO+1h_rep3 |
| Sample type |
SRA |
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| Source name |
Forelimb bud
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| Organism |
Mus musculus |
| Characteristics |
tissue: Forelimb bud
genotype: WT Swiss Albino
treatment: DMSO
timepoint of_treatment: E10.5
timepoint of_dissection: E10.5 + 1hour
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Limb buds were dissected in ice-cold PBS, washed in PBS, transferred to RNAlater (Invitrogen), and stored overnight at -20°C. The next day, samples were transferred to -80°C for long-term storage. RNA isolation was performed with the RNeasy Kit (Qiagen) following manufacture instructions. After performing QC on a Fragment Analyzer (Advanced Analytical Technologies, Inc.), RNA was stored at -80 until shipping to Novogene.
Library constructions and sequencing were performed at Novogene.
Standard Illumina mRNA-libraries (by polyA-enrichment) were made and after successful QC sequenced. Libraries were sequenced as PE150 on a NovaSeq6000 (by Novogene)
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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 |
Low quality bases and Truseq adapters were removed with cutadapt v1.16 (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 30 -m 15)
Reads were mapped on mm10 with STAR version 2.7.0e using ENCODE parameters using custom gtf https://doi.org/10.5281/zenodo.7510406, counts and coverage were computed at the same time.
FPKM values were computed with cufflinks version 2.2.1 (--max-bundle-length 10000000 --multi-read-correct --library-type "fr-unstranded" -b /home/ldelisle/genomes/fasta/mm10.fa --no-effective-length-correction -M MTmouse.gtf -G custom.gtf)
Average coverage between replicates was computed with bigwigAverage from deepTools version 3.5.5
Assembly: mm10
Supplementary files format and content: bw: normalized coverage on uniquely mapped reads
Supplementary files format and content: AllCufflinks_Simplified_timecourse.txt.gz: table with all FPKM values (one row per ensembl id, one column per sample)
Supplementary files format and content: AllHTSeqCounts_subset_timecourse.txt.gz: table with all count values obtained with STAR (one row per ensembl id, one column per sample, genes on chrX, Y, M were removed)
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| Submission date |
Aug 27, 2024 |
| Last update date |
Aug 30, 2024 |
| Contact name |
Lucille Lopez-Delisle |
| E-mail(s) |
lucille.delisle@epfl.ch
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| Organization name |
EPFL
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| Street address |
Station 19
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE275783 |
Synchronization of growth and self-organizing digit pattern by WNT signaling [RNAseq] |
| GSE275784 |
Synchronization of growth and self-organizing digit pattern by WNT signaling |
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| Relations |
| BioSample |
SAMN43383088 |
| SRA |
SRX25842458 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8484502_RNA_FL_timecourse_E10.5+DMSO+1h_rep3_Uniq_norm.bw |
136.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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