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non-target RNA-Seq in Ribo-STAMP-293T



non-target      shRNA in Ribo-STAMP-293T      Control:

General Information

List KD experiments controlled by BGRSDLV03-3dox and BGRSDLV03-4dox


NT-BGRSDLV03-3dox,NT-BGRSDLV03-4dox:
  • CNOT4-BGRSDLV03-RSD293
  • CPSF4-BGRSDLV03-RSD293
  • ERI2-BGRSDLV03-RSD293
  • FUS-BGRSDLV03-RSD293
  • MBNL1-BGRSDLV03-RSD293
  • RNF113A-BGRSDLV03-RSD293
  • RNF14-BGRSDLV03-RSD293
  • WBP4-BGRSDLV03-RSD293
  • ZC3H3-BGRSDLV03-RSD293




    • Experiment Information (Status: Submitted)
    BGRSDLV03-3doxBGRSDLV03-4dox
    idx00
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGRSDLV03-3doxBGRSDLV03-4dox
    transduction_Date9/29/239/29/23
    days4 days4 days
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc00
    WB_result
    Ave_WB
    WB_DONE_date
    MW
    IP
    antibody_Cat#
    Antibody DCC ID
    submitted_to_DCC_date
    Rep1_TPM00
    Rep2_TPM00
    ActionReadyReady
    Library_start_date
    repeat_library
    Note
    ID93179318




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGRSDLV03-3doxBGRSDLV03-4dox
    Sample_IDBGRSDLV03-3doxBGRSDLV03-4dox
    Sample Name
    Sample NameNT-BGRSDLV03-3doxNT-BGRSDLV03-4dox
    RBPnon-targetnon-target
    Cell_LineDOX-RS293DOX-RS293
    Exp UID
    StatusSubmittedSubmitted
    Status_date2024-12-032024-12-03
    ProjectENCORE2ENCORE2
    Note
    ID1260012601




    Library-Prep Information
    BGRSDLV03-3doxBGRSDLV03-4dox
    Sample #34
    Sample NameNT-BGRSDLV03-3doxNT-BGRSDLV03-4dox
    Sample_Name_Alias
    Index Well PositionC05D05
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-10-172023-10-17
    Lib_IDLib-231017Lib-231017
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp270278
    Peak_Molarity53.8043.30
    libSampleQC_DNA_WellDNA_Library_set66/set1/C6.pngDNA_Library_set66/set1/D6.png
    RIN9.89.8
    libSample_RNA_WellRNA_Library_set66/set1/C1.pngRNA_Library_set66/set1/D1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-10-182023-10-18
    Sample_IDBGRSDLV03-3doxBGRSDLV03-4dox
    RBPNTNT
    Batch_IDBGRSDLV03BGRSDLV03
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID40364037




    Sequencing Information
    BGRSDLV03-3doxBGRSDLV03-4dox
    Sample_IDBGRSDLV03-3doxBGRSDLV03-4dox
    Sample NameNT-BGRSDLV03-3doxNT-BGRSDLV03-4dox
    Pool IDPool-231018Pool-231018
    LocalServer_folderset66set66
    total_reads16,695,22622,592,850
    total_aligned_reads14,568,65119,141,551
    unique_aligned_reads13,446,04117,674,532
    percent_uniqueAligned0.805380.78231
    correlation_replicates0.9952750.995275
    spikein_reads5,6023,936
    percent_spikeins0.000340.00017
    original_ReadLength101101
    QC_StatusSubmittedSubmitted
    ID27552756




    Data Submission Information
    DCC submission information was not avaliable




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set66/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2755NovaSeq6000100paired-ended1ENCORE28928
    NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set66/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2755NovaSeq6000100paired-ended2ENCORE28968
    NT-BGRSDLV03-3dox_Aligned.sortedByCoord.out.bamENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2755GRCh38V40NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29008
    NT-BGRSDLV03-3dox_Signal.Unique.strand+.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2755GRCh38V40NT-BGRSDLV03-3dox/Aligned.sortedByCoord.out.bamENCORE29048
    NT-BGRSDLV03-3dox_Signal.Unique.strand-.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2755GRCh38V40NT-BGRSDLV03-3dox/Aligned.sortedByCoord.out.bamENCORE29088
    NT-BGRSDLV03-3dox_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2755GRCh38V40NT-BGRSDLV03-3dox/Aligned.sortedByCoord.out.bamENCORE29128
    NT-BGRSDLV03-3dox_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2755GRCh38V40NT-BGRSDLV03-3dox/Aligned.sortedByCoord.out.bamENCORE29168
    NT-BGRSDLV03-3dox_quant.sfENCODE_DATA/set66/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2755GRCh38V40NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29208
    NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set66/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2756NovaSeq6000100paired-ended1ENCORE28929
    NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set66/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2756NovaSeq6000100paired-ended2ENCORE28969
    NT-BGRSDLV03-4dox_Aligned.sortedByCoord.out.bamENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2756GRCh38V40NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gzENCORE29009
    NT-BGRSDLV03-4dox_Signal.Unique.strand+.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2756GRCh38V40NT-BGRSDLV03-4dox/Aligned.sortedByCoord.out.bamENCORE29049
    NT-BGRSDLV03-4dox_Signal.Unique.strand-.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2756GRCh38V40NT-BGRSDLV03-4dox/Aligned.sortedByCoord.out.bamENCORE29089
    NT-BGRSDLV03-4dox_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2756GRCh38V40NT-BGRSDLV03-4dox/Aligned.sortedByCoord.out.bamENCORE29129
    NT-BGRSDLV03-4dox_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2756GRCh38V40NT-BGRSDLV03-4dox/Aligned.sortedByCoord.out.bamENCORE29169
    NT-BGRSDLV03-4dox_quant.sfENCODE_DATA/set66/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2756GRCh38V40NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gzENCORE29209