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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 12, 2023 |
| Title |
easyCLIP_NoEpitope_2 |
| Sample type |
SRA |
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| Source name |
Testes
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Testes
genotype: w1118
rip antibody: anti-GFP (mouse, Millipore Sigma #11814460001)
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| Treatment protocol |
Due to complexity of protocol, please check methods on this publication for details: Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase. Baker CC, Gallicchio L, Matias NR, Porter DF, Parsanian L, Taing E, Tam C, Fuller MT. Development. 2023 Oct 27:dev.201709. doi: 10.1242/dev.201709
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| Growth protocol |
Flies were raised at 25C
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| Extracted molecule |
other |
| Extraction protocol |
Due to complexity of protocol, please check methods on this publication for details: Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase. Baker CC, Gallicchio L, Matias NR, Porter DF, Parsanian L, Taing E, Tam C, Fuller MT. Development. 2023 Oct 27:dev.201709. doi: 10.1242/dev.201709
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| Library strategy |
RIP-Seq |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
easyCLIP
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| Data processing |
cutadapt was used to trim the reads and move the UMI to the read name: cutadapt -ACTGTCTCTTATACACATCTGACGCTGCCGACGANNNNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG –pair-filter=any -u 13 -U 10 -j 1 –rename=“{id}__{r1.cut_prefix}-{r2.cut_prefix}” –minimum-length 14 -o $Output1 -p $Output2 $Input1 $Input2
Reads were mapped to the Drosophila melanogaster genome build dm6 using STAR. Reads that fell within gene regions were counted with STAR using Ensembl annotation BDGP6.84. star_pass1: STAR –runThreadN 4 –runMode alignReads –genomeDir $star_index –alignSJoverhangMin 10 –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –readFilesIn $Input1_trimmed $Input2_trimmed –outFileNamePrefix $pass1_prefix –outSAMtype None. star_pass2: STAR –runThreadN 4 –runMode alignReads –quantMode GeneCounts –genomeDir $star_index –alignIntronMax 100000 –alignMatesGapMax 100000 –outFilterMismatchNoverLmax 0.04 –sjdbFileChr- StartEnd $junction –readFilesIn $Input1_trimmed $Input2_trimmed –out- SAMtype BAM SortedByCoordinate –limitBAMsortRAM 10000000000 –outFileNamePrefix $pass2_prefix
Duplicates were removed using samtools followed by umi_tools: samtools view –bam -h -F 256 -f 64 -F 4 -q 10 -o $Output1 $Input; samtools index $Output1; umi_tools dedup –stdin=$Output1 –stdout= $Output2 –umi-separator=“__” –extract-umi-method=read_id
Samtools was used to create .bw files for visualization: bamCoverage -b $Input -o $Output –binSize 1 –normalizeUsing CPM -p 4
Reads that fell within gene regions were counted with featureCounts using Ensembl annotation BDGP6.84: featureCounts -t exon -g gene_id -p -a $gtf_file -o $Output $Input
Assembly: Ensembl annotation BDGP6.84
Supplementary files format and content: bamCoverage output: bw files for visualization
Supplementary files format and content: featureCounts output: ReadsPerGene
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| Submission date |
Nov 09, 2023 |
| Last update date |
Nov 12, 2023 |
| Contact name |
Neuza Reis Matias |
| E-mail(s) |
nmatias@stanford.edu
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| Organization name |
Stanford University
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| Department |
Developmental Biology
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| Lab |
Margaret T. Fuller
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| Street address |
279 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL25244 |
| Series (2) |
| GSE247385 |
Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase [easyCLIP] |
| GSE247388 |
Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase |
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| Relations |
| BioSample |
SAMN38180842 |
| SRA |
SRX22455467 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7888340_NoEpitope_2_R1_cut_Aligned.sortedByCoord.out.dedup.bw |
340.2 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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