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non-target RNA-Seq in K562



non-target      CRISPR in K562      Control:

General Information

List KD experiments controlled by BGKcLV37-1 and BGKcLV37-2


NT-BGKcLV37-1,NT-BGKcLV37-2:
  • DDX5-BGKcLV37-K562
  • DDX50-BGKcLV37-K562
  • DDX54-BGKcLV37-K562
  • DDX56-BGKcLV37-K562
  • NUP153-BGKcLV37-K562
  • PARP1-BGKcLV37-K562
  • PCF11-BGKcLV37-K562
  • SRP72-BGKcLV37-K562
  • SRPK1-BGKcLV37-K562
  • SRPRA-BGKcLV37-K562
  • SRPRB-BGKcLV37-K562
  • TARS-BGKcLV37-K562
  • USP10-BGKcLV37-K562
  • VARS-BGKcLV37-K562




    • Experiment Information (Status: Submitting)
    BGKcLV37-1BGKcLV37-2
    idx13531354
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequence
    PAM
    Namenon-targetnon-target
    Sample_IDBGKcLV37-1BGKcLV37-2
    transduction_Date9/20/229/20/22
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc01731
    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
    ID55015502




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV37-1BGKcLV37-2
    Sample_IDBGKcLV37-1BGKcLV37-2
    Sample Name
    Sample NameNT-BGKcLV37-1NT-BGKcLV37-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusSubmittingSubmitting
    Status_date2023-04-142023-04-14
    ProjectENCORE2ENCORE2
    Note
    ID1108211083




    Library-Prep Information
    BGKcLV37-1BGKcLV37-2
    Sample #2122
    Sample NameNT-BGKcLV37-1NT-BGKcLV37-2
    Sample_Name_Alias
    Index Well PositionE03F03
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-01-132023-01-13
    Lib_IDLib-230113Lib-230113
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp300302
    Peak_Molarity54.5065.90
    libSampleQC_DNA_WellDNA_Library_set54-56/set1/E3.pngDNA_Library_set54-56/set1/F3.png
    RIN9.79.9
    libSample_RNA_WellRNA_Library_set54-56/set1/E3.pngRNA_Library_set54-56/set1/F3.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-01-272023-01-27
    Sample_IDBGKcLV37-1BGKcLV37-2
    RBPNTNT
    Batch_IDBGKcLV37BGKcLV37
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID33923393




    Sequencing Information
    BGKcLV37-1BGKcLV37-2
    Sample_IDBGKcLV37-1BGKcLV37-2
    Sample NameNT-BGKcLV37-1NT-BGKcLV37-2
    Pool IDPool-230130Pool-230130
    LocalServer_folderset55set55
    total_reads53,853,85542,194,520
    total_aligned_reads47,706,42939,823,161
    unique_aligned_reads44,237,76336,997,442
    percent_uniqueAligned0.821440.87683
    correlation_replicates0.9975450.997545
    spikein_reads2,5424,170
    percent_spikeins0.000050.00010
    original_ReadLength101101
    QC_StatusSubmittingSubmitting
    ID22652266




    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-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2265NovaSeq6000100paired-ended1ENCORE28388
    NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2265NovaSeq6000100paired-ended2ENCORE28438
    NT-BGKcLV37-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2265GRCh38V40NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225629
    NT-BGKcLV37-1_Signal.Unique.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2265GRCh38V40NT-BGKcLV37-1/Aligned.sortedByCoord.out.bamENCORE225679
    NT-BGKcLV37-1_Signal.Unique.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2265GRCh38V40NT-BGKcLV37-1/Aligned.sortedByCoord.out.bamENCORE225729
    NT-BGKcLV37-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2265GRCh38V40NT-BGKcLV37-1/Aligned.sortedByCoord.out.bamENCORE225779
    NT-BGKcLV37-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2265GRCh38V40NT-BGKcLV37-1/Aligned.sortedByCoord.out.bamENCORE225829
    NT-BGKcLV37-1_quant.sfENCODE_DATA/set55/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2265GRCh38V40NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225879
    NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2266NovaSeq6000100paired-ended1ENCORE28389
    NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2266NovaSeq6000100paired-ended2ENCORE28439
    NT-BGKcLV37-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2266GRCh38V40NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225630
    NT-BGKcLV37-2_Signal.Unique.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2266GRCh38V40NT-BGKcLV37-2/Aligned.sortedByCoord.out.bamENCORE225680
    NT-BGKcLV37-2_Signal.Unique.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2266GRCh38V40NT-BGKcLV37-2/Aligned.sortedByCoord.out.bamENCORE225730
    NT-BGKcLV37-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2266GRCh38V40NT-BGKcLV37-2/Aligned.sortedByCoord.out.bamENCORE225780
    NT-BGKcLV37-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2266GRCh38V40NT-BGKcLV37-2/Aligned.sortedByCoord.out.bamENCORE225830
    NT-BGKcLV37-2_quant.sfENCODE_DATA/set55/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2266GRCh38V40NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225880