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| Status |
Public on Jul 31, 2021 |
| Title |
RNA-seq FL bud E9.75 replicate 3 |
| Sample type |
SRA |
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| Source name |
forelimb buds
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| Organism |
Mus musculus |
| Characteristics |
strain: Swiss albino
tissue: forelimb buds
developmental stage: E9.75
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| Extracted molecule |
total RNA |
| Extraction protocol |
Per biological triplicates (n=3), a pair of mouse forelimb buds at E9.75 (28-30 somites), E10.5 (34-36 somites) and E11.5 (43-45 somites) stages and chicken wing buds at HH20, HH22 and HH24 stages and were microdissected in cold PBS. These samples were transferred to RNA later (SigmaR0901) after an overnight incubation at 4°C and samples were stored at -20°C. Total RNA was extracted using the RNeasy micro kit (Qiagen Ref.74004). Homogenization of tissue in RLT buffer was done by sheering the sample using a 25G needle for 20 times. An on column DNA digestion (Qiagen Ref.79254) was done during the extraction to minimize the gDNA contamination. RNA integrity was checked on a Agilent Fragment Analyser (RNA analysis kit DNF-472-0500). The RNA concentration was measured by QubitTM RNA HS Assay kit (Ref Q32855).
500ng total RNA was used to prepare RNA-seq libraries using NEB non directional NEBNext® Ultra™ II RNA Library Prep (E7775), using the polyA mRNA workflow and 9 cycles of PCR amplification. Barcoded poly-A RNA-seq libraries were pooled equal molar and sequenced on the Illumina Nextseq500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
HFK5FBGX5_E975C
HV2VFBGX3_E975C
RNA_FL_E9.75_repC
Total RNA extracted from forelimb buds of mouse at E9.75 stage
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| Data processing |
Raw single-end sequencing reads of 85 bp for mouse FLB (E9.75, E10.5 and E11.5) and chicken wing bud (HH20, HH22, HH24) were subjected to quality check using FASTQC (FastQC: a quality control tool for high throughput sequence data) and Trim Galore v 0.4.1.
High-quality sequencing reads were aligned on reference genome and transcriptome (ensembl release-91) of mouse (mm10) and chicken (galGal5) using a fast accurate aligner STAR v2.5.2 (Dobin A et al., 2012) following ENCODE settings.
bigWig profiles of normalized counts (reads per kilobase per million mapped reads) were generated using deeptools v3.0.0 (Ramírez, Fidel, et al., 2016).
Genome_build: mm10, galGal5
Supplementary_files_format_and_content: bigWig
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| Submission date |
Jan 13, 2021 |
| Last update date |
Jul 31, 2021 |
| Contact name |
Shalu Jhanwar |
| E-mail(s) |
shalu.jhanwar@unibas.ch
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| Organization name |
University of Basel
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| Department |
Department of Biomedicine
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| Street address |
Mattenstrasse 28
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE164737 |
Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [RNA-seq] |
| GSE164738 |
Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development |
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| Relations |
| BioSample |
SAMN17306514 |
| SRA |
SRX9843131 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5017905_E975CAligned_dpProfiles_RNA.bw |
22.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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