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Status |
Public on Sep 13, 2023 |
Title |
3-150-2_Prog_N1: progenitors, wildtype core // progenitors, rep 1 |
Sample type |
SRA |
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|
Source name |
Isolated from wildtype Achilles tendon
|
Organism |
Mus musculus |
Characteristics |
tissue: Isolated from wildtype Achilles tendon cell type: Tendon progenitors (mixed) genotype: B6.129S2-Il6tm1Kopf/J Il-6+/+ treatment: in a hydrogel surrounding a wildtyp core explant
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Treatment protocol |
Treatment consisted of co-culture with different extrinsic cell populations and integration of core explants unable to express interleukin-6 (IL-6)
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Growth protocol |
Hybrid explant // hydrogel constructs were clamped and maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS), antibiotics, and L-ascorbic acid (200 μM) in humidified atmosphere with 5% CO2 at 37C for 7 days
|
Extracted molecule |
total RNA |
Extraction protocol |
The samples were snap-frozen in liquid nitrogen, pulverized by cryogenic grinding (FreezerMill 6870, SPEXTMSamplePrep), and further processed with the RNeasy micro kit (Qiagen) The RNA libraries were prepared using Illumina's Stranded Total RNA Prep with Ribo-Zero Plus.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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|
Description |
Illumina Truseq Total RNA (ribosomal depletion)
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Data processing |
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) or reads shorter than 30nt using Fastp (v0.20). Pseudoalignment and calculation of transcript abundance based on the high quality reads was performed with Kallisto (v0.46.1) using the GENCODE annotation of release M26 for the mouse genome GRCm39. Differential expression analysis was performed with DESeq2 (R4.1.2, v1.34). All previous steps were performed using the SUSHI framework at the Functional Genomics Center Zurich. Assembly: GRCm39 Supplementary files format and content: .txt : text file containing trancript identifiers (ENSEMBL ID) and the match counts based on Kallisto Supplementary files format and content: .xlsx : Microsoft Excel Worksheet containing the DEG data based on DESeq2 (i.e. gene_id, gene_name, GO, gnc_symbol, entrez_id, log2 ratio, pValue, fdr)
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Submission date |
Sep 23, 2022 |
Last update date |
Sep 13, 2023 |
Contact name |
Tino Stauber |
E-mail(s) |
staubert42@gmail.com
|
Organization name |
ETH Zurich
|
Street address |
Lengghalde 5
|
City |
Zurich |
ZIP/Postal code |
8008 |
Country |
Switzerland |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE214015 |
Il-6 signaling exacerbates hallmarks of tendon lesions by stimulating progenitor proliferation & migration to damage. |
|
Relations |
BioSample |
SAMN30983651 |
SRA |
SRX17681523 |