non-target      CRISPR in K562      Control: NT-BGKcLV11

General Information

List KD experiments controlled by BGKcLV11-1 and BGKcLV11-2


NT-BGKcLV11-1,NT-BGKcLV11-2:
  • ACO1-BGKcLV11-K562
  • CIRBP-BGKcLV11-K562
  • G3BP1-BGKcLV11-K562
  • NCBP1-BGKcLV11-K562
  • NIP7-BGKcLV11-K562
  • PES1-BGKcLV11-K562
  • RBM25-BGKcLV11-K562
  • RPLP0-BGKcLV11-K562
  • SF3B1-BGKcLV11-K562
  • SRSF5-BGKcLV11-K562
  • STAU2-BGKcLV11-K562
  • TRA2A-BGKcLV11-K562
  • XRCC5-BGKcLV11-K562
  • ZC3H11A-BGKcLV11-K562




    • Experiment Information (Status: Released)
    BGKcLV11-1BGKcLV11-2
    idx317318
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGKcLV11-1BGKcLV11-2
    transduction_Date8/3/188/3/18
    daysDay 6Day 6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc05337
    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_date03/13/1903/13/19
    repeat_library
    Note
    ID44174418




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV11-1BGKcLV11-2
    Sample_IDBGKcLV11-1BGKcLV11-2
    Sample NameNT-BGKcLV11-1NT-BGKcLV11-2
    Sample NameNT-BGKcLV11-1NT-BGKcLV11-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusReleasedReleased
    Status_date2020-11-062020-11-06
    ProjectENCODE4ENCODE4
    Note
    ID26732674




    Library-Prep Information
    BGKcLV11-1BGKcLV11-2
    Sample #12
    Sample NameNT-BGKcLV11-1NT-BGKcLV11-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2019-03-132019-03-13
    Lib_IDLib-190313Lib-190313
    Tecan_Location1-A11-B1
    Tecan38.9836.97
    Tecan_date2019-03-132019-03-13
    Size_bp291289
    Peak_Molarity49.6037.30
    libSampleQC_DNA_WellDNA_Library_set42/set1/A1.pngDNA_Library_set42/set1/B1.png
    RIN9.19.4
    libSample_RNA_WellRNA_Library_set42/set1/A1.pngRNA_Library_set42/set1/B1.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2019-03-132019-03-13
    Sample_IDBGKcLV11-1BGKcLV11-2
    RBPNTNT
    Batch_IDBGKcLV11BGKcLV11
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID12




    Sequencing Information
    BGKcLV11-1BGKcLV11-2
    Sample_IDBGKcLV11-1BGKcLV11-2
    Sample NameNT-BGKcLV11-1NT-BGKcLV11-2
    Pool IDPool-190423Pool-190423
    LocalServer_folderset42set42
    total_reads95,644,17655,287,308
    total_aligned_reads91,606,82852,678,990
    unique_aligned_reads83,265,95647,938,648
    percent_uniqueAligned0.870580.86708
    correlation_replicates0.9950910.995091
    spikein_reads74,67865,824
    percent_spikeins0.000780.00119
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID4546




    Data Submission Information
    BGKcLV11-1BGKcLV11-1BGKcLV11-1BGKcLV11-1BGKcLV11-1BGKcLV11-2BGKcLV11-2BGKcLV11-2BGKcLV11-2
    ENCODE_aliasbrenton-graveley:NT-BGKcLV11brenton-graveley:NT-BGKcLV11-1brenton-graveley:L-NT-BGKcLV11-1brenton-graveley:NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV11-2brenton-graveley:L-NT-BGKcLV11-2brenton-graveley:NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR292PXVENCBS421LROENCLB108KVMENCFF879OQJENCFF762MRAENCBS390OYBENCLB999FUKENCFF430UBMENCFF256ISO
    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_IDBGKcLV11-1BGKcLV11-1BGKcLV11-1BGKcLV11-1BGKcLV11-1BGKcLV11-2BGKcLV11-2BGKcLV11-2BGKcLV11-2
    Sample NameNT-BGKcLV11-1NT-BGKcLV11-1NT-BGKcLV11-1NT-BGKcLV11-1NT-BGKcLV11-1NT-BGKcLV11-2NT-BGKcLV11-2NT-BGKcLV11-2NT-BGKcLV11-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-20
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV42_biosample_protocolLV42_library_protocolLV42_biosample_protocolLV42_library_protocol
    protocol_URLNT-BGKcLV11-1.pdfL-NT-BGKcLV11-1.pdfNT-BGKcLV11-2.pdfL-NT-BGKcLV11-2.pdf
    ID76682790999510778289109961078




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab45NovaSeq6000100paired-ended1ENCODE4377
    NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab45NovaSeq6000100paired-ended2ENCODE4459
    NT-BGKcLV11-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab45GRCh38V40NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223716
    NT-BGKcLV11-1_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab45GRCh38V40NT-BGKcLV11-1/Aligned.sortedByCoord.out.bamENCORE223798
    NT-BGKcLV11-1_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab45GRCh38V40NT-BGKcLV11-1/Aligned.sortedByCoord.out.bamENCORE223880
    NT-BGKcLV11-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab45GRCh38V40NT-BGKcLV11-1/Aligned.sortedByCoord.out.bamENCORE223962
    NT-BGKcLV11-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab45GRCh38V40NT-BGKcLV11-1/Aligned.sortedByCoord.out.bamENCORE224044
    NT-BGKcLV11-1_quant.sfENCODE_DATA/set42/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab45GRCh38V40NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224126
    NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab46NovaSeq6000100paired-ended1ENCODE4378
    NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab46NovaSeq6000100paired-ended2ENCODE4460
    NT-BGKcLV11-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab46GRCh38V40NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223717
    NT-BGKcLV11-2_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab46GRCh38V40NT-BGKcLV11-2/Aligned.sortedByCoord.out.bamENCORE223799
    NT-BGKcLV11-2_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab46GRCh38V40NT-BGKcLV11-2/Aligned.sortedByCoord.out.bamENCORE223881
    NT-BGKcLV11-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab46GRCh38V40NT-BGKcLV11-2/Aligned.sortedByCoord.out.bamENCORE223963
    NT-BGKcLV11-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab46GRCh38V40NT-BGKcLV11-2/Aligned.sortedByCoord.out.bamENCORE224045
    NT-BGKcLV11-2_quant.sfENCODE_DATA/set42/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab46GRCh38V40NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224127