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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 BGRSLV03-1 and BGRSLV03-2


NT-BGRSLV03-1,NT-BGRSLV03-2:
  • APEX2-BGRSLV03-RS293
  • CDCA7-BGRSLV03-RS293
  • CISD1-BGRSLV03-RS293
  • CISD2-BGRSLV03-RS293
  • CNBP-BGRSLV03-RS293
  • CPSF4-BGRSLV03-RS293
  • CXXC1-BGRSLV03-RS293
  • DTX3L-BGRSLV03-RS293
  • EGLN1-BGRSLV03-RS293
  • GIN1-BGRSLV03-RS293
  • NR5A2-BGRSLV03-RS293
  • SNRNP48-BGRSLV03-RS293
  • ZC3H3-BGRSLV03-RS293
  • ZFP36L1-BGRSLV03-RS293
  • ZMAT3-BGRSLV03-RS293
  • ZMAT5-BGRSLV03-RS293
  • ZNF2-BGRSLV03-RS293
  • ZNF277-BGRSLV03-RS293
  • ZNF317-BGRSLV03-RS293
  • ZNF706-BGRSLV03-RS293




    • Experiment Information (Status: Submitted)
    BGRSLV03-1BGRSLV03-2
    idx00
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequence
    PAM
    Namenon-targetnon-target
    Sample_IDBGRSLV03-1BGRSLV03-2
    transduction_Date1/30/231/30/23
    daysD4D4
    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
    ID83118312




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGRSLV03-1BGRSLV03-2
    Sample_IDBGRSLV03-1BGRSLV03-2
    Sample Name
    Sample NameNT-BGRSLV03-1NT-BGRSLV03-2
    RBPnon-targetnon-target
    Cell_LineRibo-STAMP-293TRibo-STAMP-293T
    Exp UID
    StatusSubmittedSubmitted
    Status_date2024-12-032024-12-03
    ProjectENCORE2ENCORE2
    Note
    ID1137011371




    Library-Prep Information
    BGRSLV03-1BGRSLV03-2
    Sample #12
    Sample NameNT-BGRSLV03-1NT-BGRSLV03-2
    Sample_Name_Alias
    Index Well PositionA07B07
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-02-152023-02-15
    Lib_IDLib-230215Lib-230215
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp293296
    Peak_Molarity18.7042.90
    libSampleQC_DNA_WellDNA_Library_set58/set1/A7.pngDNA_Library_set58/set1/B7.png
    RIN9.49.6
    libSample_RNA_WellRNA_Library_set58/set1/A1.pngRNA_Library_set58/set1/B1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-02-172023-02-17
    Sample_IDBGRSLV03-1BGRSLV03-2
    RBPNTNT
    Batch_IDBGRSLV03BGRSLV03
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID35083509




    Sequencing Information
    BGRSLV03-1BGRSLV03-2
    Sample_IDBGRSLV03-1BGRSLV03-2
    Sample NameNT-BGRSLV03-1NT-BGRSLV03-2
    Pool IDPool-230217Pool-230217
    LocalServer_folderset58set58
    total_reads38,519,91648,675,153
    total_aligned_reads18,703,16034,157,095
    unique_aligned_reads17,308,88231,705,837
    percent_uniqueAligned0.449350.65138
    correlation_replicates0.9934080.993408
    spikein_reads163,508295,770
    percent_spikeins0.004240.00608
    original_ReadLength101101
    QC_StatusSubmittedSubmitted
    ID23792380




    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-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set58/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2379NovaSeq6000100paired-ended1ENCORE28148
    NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set58/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2379NovaSeq6000100paired-ended2ENCORE28190
    NT-BGRSLV03-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2379GRCh38V40NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE211269
    NT-BGRSLV03-1_Signal.Unique.strand+.bwENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2379GRCh38V40NT-BGRSLV03-1/Aligned.sortedByCoord.out.bamENCORE211311
    NT-BGRSLV03-1_Signal.Unique.strand-.bwENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2379GRCh38V40NT-BGRSLV03-1/Aligned.sortedByCoord.out.bamENCORE211353
    NT-BGRSLV03-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2379GRCh38V40NT-BGRSLV03-1/Aligned.sortedByCoord.out.bamENCORE211395
    NT-BGRSLV03-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2379GRCh38V40NT-BGRSLV03-1/Aligned.sortedByCoord.out.bamENCORE211437
    NT-BGRSLV03-1_quant.sfENCODE_DATA/set58/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2379GRCh38V40NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE211479
    NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set58/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2380NovaSeq6000100paired-ended1ENCORE28149
    NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set58/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2380NovaSeq6000100paired-ended2ENCORE28191
    NT-BGRSLV03-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2380GRCh38V40NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE211270
    NT-BGRSLV03-2_Signal.Unique.strand+.bwENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2380GRCh38V40NT-BGRSLV03-2/Aligned.sortedByCoord.out.bamENCORE211312
    NT-BGRSLV03-2_Signal.Unique.strand-.bwENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2380GRCh38V40NT-BGRSLV03-2/Aligned.sortedByCoord.out.bamENCORE211354
    NT-BGRSLV03-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2380GRCh38V40NT-BGRSLV03-2/Aligned.sortedByCoord.out.bamENCORE211396
    NT-BGRSLV03-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2380GRCh38V40NT-BGRSLV03-2/Aligned.sortedByCoord.out.bamENCORE211438
    NT-BGRSLV03-2_quant.sfENCODE_DATA/set58/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2380GRCh38V40NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE211480