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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 |
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