non-target      CRISPR in K562      Control: NT-BGKcLV08

General Information

List KD experiments controlled by BGKcLV08-1 and BGKcLV08-2


NT-BGKcLV08-1,NT-BGKcLV08-2:
  • CDC40-BGKcLV08-K562
  • CENPI-BGKcLV08-K562
  • DDX20-BGKcLV08-K562
  • DDX42-BGKcLV08-K562
  • DDX59-BGKcLV08-K562
  • DDX6-BGKcLV08-K562
  • ETF1-BGKcLV08-K562
  • FUBP3-BGKcLV08-K562
  • NIPBL-BGKcLV08-K562
  • NOLC1-BGKcLV08-K562
  • PRPF8-BGKcLV08-K562
  • RPL23A-BGKcLV08-K562
  • RPS11-BGKcLV08-K562
  • SRSF3-BGKcLV08-K562
  • YWHAG-BGKcLV08-K562
  • ZNF106-BGKcLV08-K562
  • GNL3-BGKcLV08-K562




    • Experiment Information (Status: Released)
    BGKcLV08-1BGKcLV08-2
    idx226227
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon -targetnon -target
    Sample_IDBGKcLV08-1BGKcLV08-2
    transduction_Date3/8/183/8/18
    daysDay 6Day 6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc29163491
    WB_resultmore
    Ave_WB
    WB_DONE_date
    MW
    IP
    antibody_Cat#
    Antibody DCC ID
    submitted_to_DCC_date
    Rep1_TPM00
    Rep2_TPM00
    ActionReadyReady
    Library_start_date7/26/187/26/18
    repeat_library
    Note
    ID43244325




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV08-1BGKcLV08-2
    Sample_IDBGKcLV08-1BGKcLV08-2
    Sample Name
    Sample NameNT-BGKcLV08-1NT-BGKcLV08-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusReleasedReleased
    Status_date2020-11-062020-11-06
    ProjectENCODE4ENCODE4
    Note
    ID61656166




    Library-Prep Information
    BGKcLV08-1BGKcLV08-2
    Sample #12
    Sample NameNT-BGKcLV08-1NT-BGKcLV08-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2018-10-012018-10-01
    Lib_IDLib-181001Lib-181001
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp291277
    Peak_Molarity43.3059.80
    libSampleQC_DNA_WellDNA_Library_set41/set2/A1.pngDNA_Library_set41/set2/B1.png
    RIN9.49.6
    libSample_RNA_WellRNA_Library_set41/set1/A1.pngRNA_Library_set41/set1/B1.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2018-07-272018-07-27
    Sample_IDBGKcLV08-1BGKcLV08-2
    RBPNTNT
    Batch_IDBGKcLV08BGKcLV08
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID851852




    Sequencing Information
    BGKcLV08-1BGKcLV08-2
    Sample_IDBGKcLV08-1BGKcLV08-2
    Sample NameNT-BGKcLV08-1NT-BGKcLV08-2
    Pool IDPool-180901Pool-180901
    LocalServer_folderset41set41
    total_reads146,243,594124,540,264
    total_aligned_reads138,302,844119,904,976
    unique_aligned_reads124,118,056107,612,176
    percent_uniqueAligned0.848710.86408
    correlation_replicates0.9984900.998490
    spikein_reads257,674224,562
    percent_spikeins0.001760.00180
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID257258




    Data Submission Information
    BGKcLV08-1BGKcLV08-1BGKcLV08-1BGKcLV08-1BGKcLV08-1BGKcLV08-2BGKcLV08-2BGKcLV08-2BGKcLV08-2
    ENCODE_aliasbrenton-graveley:NT-BGKcLV08brenton-graveley:NT-BGKcLV08-1brenton-graveley:L-NT-BGKcLV08-1brenton-graveley:NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV08-2brenton-graveley:L-NT-BGKcLV08-2brenton-graveley:NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR015KGTENCBS671ALYENCLB181LLLENCFF844QHPENCFF893KZDENCBS727VBWENCLB527EKGENCFF099LFXENCFF307AQU
    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_IDBGKcLV08-1BGKcLV08-1BGKcLV08-1BGKcLV08-1BGKcLV08-1BGKcLV08-2BGKcLV08-2BGKcLV08-2BGKcLV08-2
    Sample NameNT-BGKcLV08-1NT-BGKcLV08-1NT-BGKcLV08-1NT-BGKcLV08-1NT-BGKcLV08-1NT-BGKcLV08-2NT-BGKcLV08-2NT-BGKcLV08-2NT-BGKcLV08-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-20
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV41_biosample_protocolLV41_library_protocolLV41_biosample_protocolLV41_library_protocol
    protocol_URLNT-BGKcLV08-1.pdfL-NT-BGKcLV08-1.pdfNT-BGKcLV08-2.pdfL-NT-BGKcLV08-2.pdf
    ID113611921262133213961193126313331397




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab257NovaSeq6000100paired-ended1ENCODE4539
    NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab257NovaSeq6000100paired-ended2ENCODE4609
    NT-BGKcLV08-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab257GRCh38V40NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE226777
    NT-BGKcLV08-1_Signal.Unique.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab257GRCh38V40NT-BGKcLV08-1/Aligned.sortedByCoord.out.bamENCORE226847
    NT-BGKcLV08-1_Signal.Unique.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab257GRCh38V40NT-BGKcLV08-1/Aligned.sortedByCoord.out.bamENCORE226917
    NT-BGKcLV08-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab257GRCh38V40NT-BGKcLV08-1/Aligned.sortedByCoord.out.bamENCORE226987
    NT-BGKcLV08-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab257GRCh38V40NT-BGKcLV08-1/Aligned.sortedByCoord.out.bamENCORE227057
    NT-BGKcLV08-1_quant.sfENCODE_DATA/set41/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab257GRCh38V40NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227127
    NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab258NovaSeq6000100paired-ended1ENCODE4540
    NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab258NovaSeq6000100paired-ended2ENCODE4610
    NT-BGKcLV08-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab258GRCh38V40NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE226778
    NT-BGKcLV08-2_Signal.Unique.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab258GRCh38V40NT-BGKcLV08-2/Aligned.sortedByCoord.out.bamENCORE226848
    NT-BGKcLV08-2_Signal.Unique.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab258GRCh38V40NT-BGKcLV08-2/Aligned.sortedByCoord.out.bamENCORE226918
    NT-BGKcLV08-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab258GRCh38V40NT-BGKcLV08-2/Aligned.sortedByCoord.out.bamENCORE226988
    NT-BGKcLV08-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab258GRCh38V40NT-BGKcLV08-2/Aligned.sortedByCoord.out.bamENCORE227058
    NT-BGKcLV08-2_quant.sfENCODE_DATA/set41/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab258GRCh38V40NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227128