run_metadata: 25177
This data as json
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| 25177 | SRR25661612 | SRX21387406 | SRS18627970 | SRP455520 | PRJNA1006302 | The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes | GSE241049 | Transcriptome Analysis | To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates. | pubmed:39658721 | hand2 OE 20 hpf CMs rep2 | GSM7714397 | source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing | hand2 OE 20 hpf CMs rep2 | Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts | embryonic heart | miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio. | tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS | GSM7714397 | GSM7714397: hand2 OE 20 hpf CMs rep2; Danio rerio; RNA Seq | GSM7714397 r1 | GSM7714397 | 1 | miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | SRP455520 | loader:fastq load.py | E22_3458_Yanli_HT_Lib_OE_CMs_2_R1.fastq.gz | fastq | 2197151812.0 | 30722639.0 | GSM7714397 r1 | 0:71.52 | A:617116635;C:461951919;G:481371246;T:636712012;N:0 | 71 | 617116635 | 461951919 | 481371246 | 636712012 | 0 | SRX21387406 | SRS18627970 | SRA1694205 | MPI for heart and lung research | MPI for heart and lung research | 1 | 0.90877 | 0.14744 | 0.77191 | 0.42845 | 72 | B | usable mapping rate | illumina | nextseq_v2 | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2023-08-17 | Segmentation | Embryo | Heart | Cardiovascular System |