non-target      CRISPR in K562      Control: NT-BGKcLV17

General Information

List KD experiments controlled by BGKcLV17-1 and BGKcLV17-2


NT-BGKcLV17-1,NT-BGKcLV17-2:
  • E4F1-BGKcLV17-K562
  • ERN1-BGKcLV17-K562
  • FBL-BGKcLV17-K562
  • GARS-BGKcLV17-K562
  • GEMIN2-BGKcLV17-K562
  • GSPT2-BGKcLV17-K562
  • IFIT2-BGKcLV17-K562
  • PDCD4-BGKcLV17-K562
  • PPP1R10-BGKcLV17-K562
  • RAE1-BGKcLV17-K562
  • SF3A1-BGKcLV17-K562
  • SMAD4-BGKcLV17-K562
  • SUZ12-BGKcLV17-K562
  • ZNF335-BGKcLV17-K562
  • ZNF574-BGKcLV17-K562
  • BAZ1A-BGKcLV17-K562
  • CTCF-BGKcLV17-K562
  • CXXC1-BGKcLV17-K562
  • DDX39B-BGKcLV17-K562
  • DHX57-BGKcLV17-K562
  • DUS3L-BGKcLV17-K562




    • Experiment Information (Status: Released)
    BGKcLV17-1BGKcLV17-2
    idx608609
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGKcLV17-1BGKcLV17-2
    transduction_Date7/2/197/2/19
    daysDay 6Day 6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc05236
    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_date12/05/1912/05/19
    repeat_library
    Note
    ID47204721




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV17-1BGKcLV17-2
    Sample_IDBGKcLV17-1BGKcLV17-2
    Sample Name
    Sample NameNT-BGKcLV17-1NT-BGKcLV17-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusReleasedReleased
    Status_date2020-12-012020-12-01
    ProjectENCODE4ENCODE4
    Note
    ID54855486




    Library-Prep Information
    BGKcLV17-1BGKcLV17-2
    Sample #7576
    Sample NameNT-BGKcLV17-1NT-BGKcLV17-2
    Sample_Name_Alias
    Index Well PositionG09H09
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2020-08-312020-08-31
    Lib_IDLib-200102Lib-200102
    Tecan_Location1-A11-B1
    Tecan21.4229.10
    Tecan_date2019-12-102019-12-10
    Size_bp272273
    Peak_Molarity30.2024.60
    libSampleQC_DNA_WellDNA_Library_set43-44/set1/A6.pngDNA_Library_set43-44/set1/B6.png
    RIN8.79.1
    libSample_RNA_WellRNA_Library_set43-44/set4/A1.pngRNA_Library_set43-44/set4/B1.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2019-12-112019-12-11
    Sample_IDBGKcLV17-1BGKcLV17-2
    RBPNTNT
    Batch_IDBGKcLV17BGKcLV17
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID651652




    Sequencing Information
    BGKcLV17-1BGKcLV17-2
    Sample_IDBGKcLV17-1BGKcLV17-2
    Sample NameNT-BGKcLV17-1NT-BGKcLV17-2
    Pool IDPool-200102Pool-200102
    LocalServer_folderset43_Kset43_K
    total_reads98,754,406110,521,278
    total_aligned_reads92,350,576106,394,606
    unique_aligned_reads84,280,37296,764,834
    percent_uniqueAligned0.853430.87553
    correlation_replicates0.9980820.998082
    spikein_reads18,06232,100
    percent_spikeins0.000180.00029
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID153154




    Data Submission Information
    BGKcLV17-1BGKcLV17-1BGKcLV17-1BGKcLV17-1BGKcLV17-1BGKcLV17-2BGKcLV17-2BGKcLV17-2BGKcLV17-2
    ENCODE_aliasbrenton-graveley:NT-BGKcLV17brenton-graveley:NT-BGKcLV17-1brenton-graveley:L-NT-BGKcLV17-1brenton-graveley:NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV17-2brenton-graveley:L-NT-BGKcLV17-2brenton-graveley:NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR516TLXENCBS935MDRENCLB314FFDENCFF144HNLENCFF853XQBENCBS813SYBENCLB798LSAENCFF063ZYPENCFF816GYE
    object_typeexperimentbiosamplelibraryfile_fastq1file_fastq2biosamplelibraryfile_fastq1file_fastq2
    assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seq
    Sample_IDBGKcLV17-1BGKcLV17-1BGKcLV17-1BGKcLV17-1BGKcLV17-1BGKcLV17-2BGKcLV17-2BGKcLV17-2BGKcLV17-2
    Sample NameNT-BGKcLV17-1NT-BGKcLV17-1NT-BGKcLV17-1NT-BGKcLV17-1NT-BGKcLV17-1NT-BGKcLV17-2NT-BGKcLV17-2NT-BGKcLV17-2NT-BGKcLV17-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-18
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV43K_biosample_protocolLV43K_library_protocolLV43K_biosample_protocolLV43K_library_protocol
    protocol_URLNT-BGKcLV17-1.pdfL-NT-BGKcLV17-1.pdfNT-BGKcLV17-2.pdfL-NT-BGKcLV17-2.pdf
    ID36154318516568155319517569




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab153NovaSeq6000100paired-ended1ENCODE4101
    NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab153NovaSeq6000100paired-ended2ENCODE4153
    NT-BGKcLV17-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab153GRCh38V40NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gzENCORE224392
    NT-BGKcLV17-1_Signal.Unique.strand+.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab153GRCh38V40NT-BGKcLV17-1/Aligned.sortedByCoord.out.bamENCORE224444
    NT-BGKcLV17-1_Signal.Unique.strand-.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab153GRCh38V40NT-BGKcLV17-1/Aligned.sortedByCoord.out.bamENCORE224496
    NT-BGKcLV17-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab153GRCh38V40NT-BGKcLV17-1/Aligned.sortedByCoord.out.bamENCORE224548
    NT-BGKcLV17-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab153GRCh38V40NT-BGKcLV17-1/Aligned.sortedByCoord.out.bamENCORE224600
    NT-BGKcLV17-1_quant.sfENCODE_DATA/set43_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab153GRCh38V40NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gzENCORE224652
    NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab154NovaSeq6000100paired-ended1ENCODE4102
    NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab154NovaSeq6000100paired-ended2ENCODE4154
    NT-BGKcLV17-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab154GRCh38V40NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gzENCORE224393
    NT-BGKcLV17-2_Signal.Unique.strand+.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab154GRCh38V40NT-BGKcLV17-2/Aligned.sortedByCoord.out.bamENCORE224445
    NT-BGKcLV17-2_Signal.Unique.strand-.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab154GRCh38V40NT-BGKcLV17-2/Aligned.sortedByCoord.out.bamENCORE224497
    NT-BGKcLV17-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab154GRCh38V40NT-BGKcLV17-2/Aligned.sortedByCoord.out.bamENCORE224549
    NT-BGKcLV17-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab154GRCh38V40NT-BGKcLV17-2/Aligned.sortedByCoord.out.bamENCORE224601
    NT-BGKcLV17-2_quant.sfENCODE_DATA/set43_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab154GRCh38V40NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gzENCORE224653